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Mexico is considered a megadiverse country, ranking second worldwide in reptile diversity. To determine the spatial and temporal variation of the reptile assemblage in El Quelele lagoon in Bahía de Banderas, Nayarit (20°43’N and 105° 17’W), we realized transects of 500 m2 for three different types of vegetation (mangrove, marshes and thorn forest) during two seasons (Dry and Rainy), We calculate the ecological indices (Shannon, Simpson and Pielou) and the biological value index. We report 19 species, representing 21.5% of the total species reported in Nayarit. The most abundant species were Anolis nebulosus, Holcosus undulata and Iguana iguana. Four species (21%) are endemic to Mexico, and nine species (47%) are registered within at-risk categories. Mangroves had the highest species richness (13 spp.), followed by marshes (9 spp.) and finally the thorn forest (5 spp.). Diversity was highest during the dry season within mangroves (H’=2.93) and in the marshes (1-D=0.93), which may be related to water availability. This study provides a foundation for reptile conservation in this area.