Significance In Baja California, the deserts meet the coastal dunes in a narrow transition visible even from satellite images. We study two species pairs of desert shrubs ( Encelia ) that occur across this transition. Although these species can interbreed, they remain distinct. Using a combination of genetics, field experiments, three-dimensional imaging, and physiological measurements, we show that natural selection helps counteract homogenizing effects of gene exchange. Different habitats of these species create multiple mechanisms of selection—drought, salinity, herbivory, and burial, which together maintain these species in their native habitats and their hybrids in intermediate habitats. This study illustrates how environmental factors influence traits and fitness and how these in turn can maintain species, highlighting the importance of natural selection in speciation.