Microbial communities of stratified phototrophic bacteria in laminated intertidal sediments north of Estuary El Puente, near San Carlos, Baja California Sur, Mexico,‐were studied. This study describes the macroscopic and microscopic characteristics of the mats, including their annual growth. The mats were located in and along meandering mangrove‐lined tidal channels. Their thickness ranged from 0.5 to 25 cm. Square‐meter areas of polygonal mats were detected in several ponds infiltrated by sea water. The principal microbial community of the upper surface of various morphotypes of microbial mats was identified as cyanobacteria belonging to the generaMicrocoleus, Lyngbya, Phormidium,andOscillatoria.Other cyanobacte‐rial genera such asPseudanabaena, Spirulina, Synechococcus,andGloeocapsa,as well as many unidentified diatoms, were also present but at lower population densities. The second inward reddish layers of the microbial mats contained similar cyano‐bacterial genera plus anoxygenic phototrophic bacteria belonging to the generaChloroflexus, Thiocapsa, Chromatium, Prosthecochloris, Rhodopseudomonas,andChlorobium,as well as several unidentified bacteria. In situ measurements on the growth of the mats, from intermittent tide sites, showed an annual buildup of two layers: green and reddish. These layers corresponded to a vertical growth of 1.4±0.27 mm/year. Permanently submerged mats did not show vertical growth during the same period of time.