Sediments in coastal wetlands host communities of phylogenetically diverse primary producers such as diatoms, cyanobacteria, and anoxygenic photosynthetic bacteria, but little is understood about spatial variation in the composition of these assemblages at the highest taxonomic levels. Using High Performance Liquid Chromatography to quantify taxon-specific pigments, I investigated habitat-linked heterogeneity in microphytobenthic biomass, composition, and diversity within two natural wetland systems from southern California and tested for differences in community structure between natural and restored ecosystems. Natural vegetated habitat at Mission Bay had higher concentrations of zeaxanthin (cyanobacteria) and bacteriochlorophyll a (anoxygenic photobacteria) than unvegetated mudflat and creek banks. Organic matter was positively correlated with the concentrations of these pigments, whereas sediment pore water salinity and sand content were generally unrelated to composition. At Tijuana Estuary, community structure was generally similar between mudflat and Spartina marsh at the natural site, but concentrations of chlorophyll a and fucoxanthin (diatoms) were higher in mudflats. Restored wetland similarity with adjacent natural habitat (age 2 yr at Tijuana Estuary and 6 yr at Mission Bay) depended on habitat type and pigment measure. Restored upper intertidal succulent marsh at Mission Bay was most divergent: it had lower microalgal biomass, a lower concentration of zeaxanthin relative to fucoxanthin, and less bacteriochlorophyll a relative to chlorophyll a than natural habitat. The results suggest that patches of prokaryotic primary producers coincide with areas of high sediment organic matter and/or hypoxia superimposed on a broadly distributed flora of diatoms across various wetland landscapes.