Epilithic biofilms play key roles in rocky shore ecosystems. The diversity and biomass of epilithic biofilms were determined along a subtropical intertidal rocky shore at Xpicob, Southern Gulf of Mexico (Campeche, Mexico). Biofilm diversity was assessed by polymerase chain reaction (PCR) amplification of partial 16 S rRNA genes using single-strand conformation polymorphism (SSCP). Triplicate 2 cm×2 cm biofilm samples per site were taken randomly from 0.6 m×0.6 m quadrats located in two sampling sites, established 20 m apart within a homogeneous calcareous intertidal platform. Twenty-two partial rRNA sequences, belonging to four bacterial divisions (Cyanobacteria, Bacteroidetes, Actinobacteria and Proteobacteria), were recovered from these biofilms; of these, cyanobacteria were the most abundant (41%). The occurrence of cyanobacterial sequences in most samples, along with the detection of high levels of chlorophyll a and phycobiliprotein, indicates that these organisms are dominant within the biofilms. Consistent with previous reports, thick-sheathed cyanobacteria such as those found in this study (Xenococcus, Myxosarcina and Chroococcidiopsis) are typical in habitats in intertidal zones. In addition, most of the detected organisms from other bacterial lineages had closest relatives displaying biofilm phenotypes that suggested stressful conditions (i.e. desiccation) prevailed in the intertidal shores; this was selecting for biofilm-forming or thick-sheathed organisms as an ecological adaptation to withstand the conditions. Unweighted pair-group method with arithmetic mean (UPGMA) analysis of SSCP profiles indicated that there was significant spatial heterogeneity in biofilm community composition across different scales of analysis and that this heterogeneity was related to the distance at which samples were taken. This analysis showed that certain organisms appeared to be station specific and that the biofilm community structure varied even on a small scale (1 cm). Since no significant differences in bulk sea water or substratum physicochemistry were observed, these results suggest that small-scale variability of environmental conditions, surface properties and/or biological interactions (i.e. allelopathy) may be important factors structuring these biofilm communities.