In order to assess the composition and spatio-temporal variation of phytoplankton in Lake Chapala, a study was carriedout at ten sampling stations in January, May and September during 2012. A total of 60 species/morphospecies of netphytoplankton were recorded at the surface and at two metres depth. The Division Chlorophyta recorded the highestnumber of species (22), followed by Cyanophyta (20), Heterokontophyta (13), Euglenophyta (four) and Dinophyta(one). Cyanophyta species accounted for 84-90% of the abundance of the five divisions in the sampling months, withslight species turnover at the order level in this class. Multidimensional scaling analysis (NMDS) showed an evidentseparation of the phytoplankton community between sampling months forming three temporal clusters, consistent withthe exploratory similarity analysis (SIMPER), which also showed three temporal associations. While Bray Curtisordination analysis revealed a significant correlation between phytoplankton species and environmental variables, such asdissolved oxygen, transparency, irradiance, temperature, pH, dissolved oxygen and wind speed (p < 0.05). In conclusion,a clear dominance in presence and abundance of species of the Cyanophyta Division was observed in the lake during thepresent study; identifying the traditional succession process in the phytoplankton community assemblages, characteristicin water bodies with different levels of eutrophication.