In spite of their ecological and economic importance, reef fishes from the coast of Oaxaca, Mexico are rarely studied, therefore precluding their management and conservation. In order to identify the set of habitat characteristics/environmental conditions that predict major shifts in fish assemblages in space and time, a stationary census (5′, φ = 5 m) was conducted on a semi-monthly basis from 2006 to 2009 at patch reefs along the coast. Habitat configuration was gathered using 25 m long point-intersect transects (data every 25 cm), recording all underlying coral species and substrate characteristics (rocks, sand, algal mats, rubble or dead corals). Recorded were 65 452 fishes grouped in 11 orders, 36 families, 65 genera and 89 species. Labridae (nine species), Pomacentridae (eight species) and Serranidae (seven species) were the most frequent families. Abundance is severely skewed among species; four species Thalassoma lucasanum, Chromis atrilobata, Apogon pacificus and Stegastes acapulcoensis comprise nearly 59% of the fish abundance, 11 species contribute 30%, whereas most of the species (75) can be considered as rare since they contribute <1% each to the total. Species richness and family-level assemblage composition are similar to those recorded elsewhere in the eastern Pacific. Non-parametric multivariate analysis of variance demonstrated that changes of diversity metrics might be associated with environmental differences on the scale of hundreds of meters to kilometers, as well as coupled with major changes on oceanographic variables throughout time, exerting meaningful changes on reef-related fish assemblages.