My pet peeve is when PCT hikers refer to the first 700 miles of the trail as "desert." Some of it is desert, but some of it isn't. Within Section A, from the border to Warner Springs, most of the trail is not actually desert. This site provides an explanation of the many different plant communities within California. Some non-desert ones that you encounter in Section A are: Chaparral, Oak Woodland, Riparian, Mixed Evergreen Forest, and Coastal Sage Scrub. A desert plant community you may encounter is creosote bush scrub.
Coastal Sage Scrub
I have a hard time distinguishing between coastal sage scrub and chaparral, but as you start the trail, you are certainly in one of the two most of the time until you nearly reach the top of Mt. Laguna. The way I've been told to tell the difference is that chaparral is woodier and harder to walk through off-trail. Some call it "elfin forest" because, to a tiny elf, it would look like an enormous forest.
Common plants in Coastal Sage Scrub are: "California Sagebrush (Artemisia californica) Buckwheat (Eriogonum spp., notably E. fasciculatum), California Lilac (Ceanothus spp.), Manzanita (Arctostaphylos spp.), Monkey flowers (Diplacus spp., the drought tolerant types), Sage (Salvia spp.), Gooseberry and Currant (Ribes spp.), Coyote Brush (Baccharis sp.)."
You certainly see these plants as you go along your first section of trail. In the early spring, the ceanothus, also known as California Lilac, is blooming everywhere. Trees are absolutely covered in white to lavender to dark blue-purple flowers. They are very hard to photograph (trust me, I've tried for years) because they are so tiny and they flutter in the wind non-stop.
Buckwheat is hard to tell apart from another plant, chamise, unless the two are blooming, but buckwheat has umbels of tiny white flowers that turn rust-colored as they dry. Even after the flowers are gone, you can see umbrella shaped umbels sticking out from the plant. Chamise also has white flowers, but they are not in umbels at all. I've seen both on the trail. The first mile or two of the PCT is covered in chamise, which should be in full bloom in May. Red and orange monkeyflowers are also common, and you''ll also see (and smell) plenty of white sage and California sagebrush.
Buckwheat flowers with tarantula hawk wasp on it on Mt. Laguna, ~ mi 48
Chamise in bloom, on the trail in the first mile
Monkeyflower at mile 3
As noted before, Chaparral is sometimes called "elfin forest." It's similar to sage scrub but it would be harder to hike cross country through it because it's woodier.
"The aspect of a hillside can make a great difference in the makeup of the chaparral. North facing slopes are a lot moister and can support Toyon (Heterromoles arbutifolia), Manzanita (Arctostaphylos spp.), Scrub oak (Quercus spp.), Pitcher sage (Lepechinia spp.), Climbing Penstemon (Kekiella cordifolia, K. antirrhinoides), and Poison oak (Toxicodendron diversilobum). The dry arid south facing slope is dominated by Chamise (Adenostoma spp.), Black sage (Salvia melifera), Yucca (Yucca spp.), Woolly blue curls (Trichostema lanatum) and Bush poppy, (Dendromecon rigida)."
Of these, I saw a lot of chamise, manzanita, scrub oak, poison oak, yucca, and woolly blue curls in the early part of the trail. The poison oak was mostly limited to wetter areas like creeks. You can tell the manzanitas by their gorgeous red bark. Woolly blue curls are one of my favorite flowers of all. I saw quite a few in the first mile of the trail.
Woolly blue curls, in the first mile of the trail
A manzanita at mile 2
More chamise, mile 3
Poison oak at mile 1. Keep an eye out for more of it at the creek at mile 4.4.
There are a few other plants I saw quite a bit in the first few miles. They include:
Basket Bush, Rhus trilobata, which some confuse with Poison Oak
Ribbonwood, also known as Red Shank, in the first mile or two of the trail
Sugar Bush, Rhus ovata, at mile 2. This shows the fruit and leaves in May.
Sugar Bush flower buds in March at mile 1
This year, you'll get to see an interesting phenomenon as you hike toward Lake Morena. When you pass the several miles that burned in the Campo fire last year, you will see a lot of "crown sprouters." The crown is the part of the plant where the roots meet the top portion of the plant. A lot of chaparral plants are adapted to burn above ground in a fire, but stay alive below ground. After the fire, they re-sprout from the crown. In March I saw several miles of nearly entirely bare ground with dead shrubs poking up all over. At the base of each, the plant was resprouting. At that time, the only other plants growing tended to be wild cucumber vines (with nothing to climb on since everything had burned) and California peonies.
Wild cucumber fruit starting to grow with its flower still intact. Note: These are NOT EDIBLE fruits
Wild cucumber flower
Sagebrush, Coast Live Oaks, Buckwheat, Elder, and Golden Yarrow around mile 21
As you hike your first miles of PCT, you also pass Riparian plant communities along streams. One example of this is right as you go under the 8 freeway, just north of Boulder Oaks. Riparian plant communities are always along streams, although sometimes the water dries up in SoCal during part of the year.
You commonly see three kinds of trees here: Cottonwoods, Sycamores, and Willows. You may also see blackberries, wild grapes, yerba mansa, California wild roses, poison oak, Douglas mugwort, cattails, and Juncus.
Blackberry near the footbridge just north of the 94, ~ mile 2
California Wild Rose, mile 24
Despite the description of Oak Woodland as containing both Coast Live Oaks and Engelmann Oaks, you'll see mostly Coast Live Oaks at the lower elevation. I saw a great example of oak woodland at Lake Morena, complete with acorn woodpeckers all over the place living on the acorns. Fred Canyon at mile 32 looked like another good example.
Coast Live Oak leaves at mile 2
Coast Live Oak at Boulder Oaks, mile 26
I thought I might have found one Engelmann Oak around mile 22. They are not very common trees. In general, most of the time you see a tree (not a shrub) and you aren't near water, it's probably a coast live oak.
Right now, our oaks are in trouble from a bug called the Gold Spotted Oak Borer. It is invasive, probably from Arizona, and scientists believe it came to California in firewood. That is why they encourage you to "buy it where you burn it" when you buy firewood. Pests can be transported in the wood. The Gold Spotted Oak Borer lays its eggs in the bark of the trees and the larvae eat the inner bark of the trees, ultimately killing the trees. Then they boroe their way out to reproduce so the next generation can kill more trees. They only like older, larger trees, so it's the big, old trees that are in trouble.
Mixed Evergreen Forest
At last you reach Mixed Evergreen Forest on Mt. Laguna. I was surprised how far up the mountain I was before I truly reached it. I hiked to mile 36 in the dark and camped there, and then I woke up the next day and continued. I don't think it was until I was really around mile 40 or so that I felt like I had at long last reached the Jeffrey and Coulter Pines and the Black Oaks (Quercus kelloggii) I associate with Mt. Laguna. Coulter Pines have pine cones the size of pineapples so they are easy to spot. Black Oaks are deciduous so they drop their leaves in the winter. Their leaves look much different from Coast Live Oak leaves. Their acorns are different too. Coast Live Oak acorns are long, skinny, and pointy, whereas Black Oak acorns are more rounded and fatter.
Black Oak leaves, mile 47
Coulter Pine on Mt. Laguna
Coulter Pine with my hiking boot in the shot to show scale
It's not until you leave Mt. Laguna that other ecosystems transition into true desert. The miles before and after Scissors Crossing (mile 77-78) are truly desert. There you will see lots of different kinds of cacti, creosote bush, cat claw acacia, honey mesquite, and other desert plants.
As you climb out of the desert in the San Felipe hills, at a certain point the landscape changes and it's not truly desert anymore. I don't know at what point that is. You go up, up, up until about mile 96, and then you start going down the other side. And THAT is where you truly see a change. It's especially remarkable from about Barrel Springs (mile 101) onward, into Warner Springs. You can see this photo below, from near mile 106, is clearly no longer desert.
It's interesting that you are hiking between about 2000 and 6000 feet in elevation for all of Section A, and you are about 50 miles inland and going north the whole way through a cross-section of San Diego county. Why is it not all desert?
The answer lies in the mountains. Think about the miles you hike on Mt. Laguna from about 43 to 49. You are at about 5800 feet looking down over a vast, dry desert. Moisture comes in from the coast and it rises and cools. A lot of the rain falls on Mt. Cuyamaca, named from the Kumeyaay word for "rainy place." What's left falls on Mt. Laguna. Very little moisture remains after that, creating the desert. But without such tall mountains to cool the air and wring all of the moisture out of it, other areas of the county that are equally far inland are not equally dry.