Invasions by non-native taxa can have severe consequences for native species. In the heavily invaded serpentine grasslands of central California, many native species appear to be restricted to isolated outcrops of shallow serpentine soil, or “hummocks,” although the extent to which these hummocks function as refuges for native vegetation has never been quantified. We tested whether native plant species were restricted to hummocks within a serpentine grassland at the University of California Sedgwick Reserve near Santa Barbara, California by sampling species along hummock-grassland gradients. We also examined the influence of soil parameters, hummock area, proximity to other hummocks, and spatial location on species composition across 16 hummocks at this site. Both the hummocks and the surrounding grassland had high Mg, low Ca, and low Ca to Mg ratios typical of serpentine systems. Hummocks appeared to be more stressful environments because of their shallower soils, lower cation exchange capacity, and greater percent sand. Of the 27 most common plant species sampled along hummock-grassland transects, we identified 8 hummock specialists, 7 edge specialists, 8 matrix specialists, and 4 generalists. Importantly, both the hummock and matrix specialist groups included native species. Plant community composition was correlated with spatial positioning of the hummocks and with soil Ca, Na, K, and N. The number of species increased and community composition changed with increasing hummock area. Species composition was most similar among hummocks in close proximity to each other, and decreased with increasing distance between hummocks. Our results suggest that the community structure of serpentine grasslands is spatially complex and an effective management or restoration plan must address this complexity.