This article constitutes an advance of the reached results in the research project entitled Installation and Operation of a Native Microalgae strains Bank for Bioremediation, Bioassays and Bioproducts. It is a response to regional needs for research and technological development, which are intended to be serviced with the operation of a conditioned laboratory that allows the isolation, identification and characterization of native species.With this orientation, it was kept a methodology whose highlights is the sampling and filtering (35 µm y 90 µm) was followed; isolation agar pipetting and scratch; the optimum culture medium turned out to be a composition of modified Conway. As a result the following species of freshwater microalgae were obtained: Chlorella sp; Haematococcus sp.; Fragilaria sp.; Scenedesmus sp.(1); Scenedesmus sp. (2); Clamydomonas sp .; and Orococus sp.As for marine species they were identified: Cyclotella sp .; and Nitzschia sp., using keys Crawford et al. (1990), Prescott (1970) and Brunel (1962). For the development of subsequent phases is recommended consolidating strategic alliances with institutions to establish routes of cooperation, strengthening exercises characterization, cultivation and distribution of the species identified.