As Chiapas state, México, counts on an extensive hydrography with diverse nutrimental and climatic characteristics, it therefore allows isolating and identifying microalgae with bioenergetics potential. For this purpose, samples from 8 locations were collected, corresponding to 6 rivers, a wastewater and a springwater. The isolation of microalgae was developed for 4 weeks with 12:12 light/dark cycles. We demonstrated that the most efficient means for the isolation of microalgae of the hydrographic areas evaluated was the medium BG11 with 80.53% effectiveness. Of the microalgal consortium identified, 90% are composed of microalgae belonging to the class Chlorophycear. It was shown that another factor favouring the richness of morphotypes identified in the Santo Domingo River is associated with adequate concentrations of macroelements such as nitrates, nitrites, ammonium, phosphorus, sodium, potassium, magnesium and calcium at concentrations of 0.03 mg/l, 0.0006 mg/l, 0.08 mg/l, 0.03 mg/l, 62.93 mg/l, 5.46 mg/l, 34.52 mg/l and 48.78 mg/l respectively and microelements such as copper, zinc, iron, andmanganese at concentrations less than 0.2 mg/l in all microelements. The identified morphotypes, according to literature, have lipid contents ranging from 2 to 90%; this is of biotechnological importance for the production of biodiesel.