Microcystis is a bloom-forming, common cyanobacterium in urban lakes of Mexico City. To assess the presence of potentially cyanotoxin-producing Microcystis, molecular techniques were applied and acute toxicity bioassays were performed with Daphnia magna neonates exposed to cyanobacterial crude extracts. Toxigenic potential of isolated strains was inferred by amplifying the mcyA-Cd genes and their identity as Microcystis was confirmed through the 16S rDNA and phycocyanin operon amplification. Microcystins synthesized under culture conditions were quantified through ELISA. The acute toxicity bioassays revealed that mortality was independent from the cyanotoxin concentration in some strains; this suggests the presence of other metabolites (different from microcystins) that also exerted an important biological effect. Isolated strains had the mcyA-Cd gene and most of them produced variable amounts of microcystins in the culture conditions used, confirming their toxigenic potential. Results warn about possible toxic effect risks for aquatic biota, neighboring areas, visitors and users of these sites, due to the constant presence of these blooms in the studied water bodies.