Phytoplankton plays a key role in aquatic ecosytems as an oxygen producer, a CO2 trap, a primary source of food in trophic chains and as an indicator of changes in the environment. However, despite this positive importance, it can also develop into harmful algal blooms. With the aim of increasing knowledge about this group of microorganisms in Mexican aquatic ecosystems, a list of the phytoplankton species of the Sontecomapan Lagoon was made indicating those that potentially can provoke red tides. Besides, the distribution and abundance of these species was studied in two seasons, the rainy one (June, 2015) and the dry one (February, 2016) on eight sampling stations. Phytoplankton samples were collected with a Van Dorn bottle to measure environmental factors (transparency, salinity, temperature, pH and dissolved oxygen). A list with 357 species with a clear dominance of diatoms (67.8%) and dinoflagellates (20.16%) was obtained from literature review and materials derived from this study. Among them, 19.88% can potentially from red tides, and some of them are toxic. From the sample collected, 102 species of phytoplankton were recorded; 42 of them during the rainy season, 65 during the dry one and 7 présents in both. Among these species, 17 can potentially form red tides and from these, only two can be toxic for humans : Dinophysis caudata and Lyngbya majuscula. The cluster analysis of the environmental factors showed the formation of four groups in the rainy season and three in the dry season, associated to teh salinity gradients.