ABSTRACT Microalgae are a highly effective and renewable source of biodiesel that can be used as a substitute for petro-diesel in the global fuel market. In the present study, 14 water samples were collected from a variety of locations along the coastal areas of the Red Sea and the Mediterranean Sea in Egypt. These water samples, which contained microalgae, were subjected to enrichment process and standard procedures to obtain pure cultures. Based on morphological features, 27 microalgae isolates representing 12 different species were identified, with Chlorella species being the most dominant. Based on 18s rRNA gene sequencing, nine new native microalgae strains were identified, comprising four strains belonging to Chlorella species, two strains to Chlamydomonas, and one strain each of Phormidium, Nostoc, and Microcytosis species that could be appropriate for producing biodiesel. This information could be used to improve the knowledge on the composition of planktonic microalgal communities of Egypt and the target native species for biodiesel production.