Ostracods are microscopic crustaceans living in a wide variety of environments. They are very important as the key food item for fish and benthic macro-invertebrates and are used as bio-indicators for environmental changes and pollution. The identification and taxonomy of the Heterocypris species are so challenging issues because of their morphological plasticity that is often related to environmental factors. The studied species is recorded for the first time in Egypt. Therefore, Morphological evidences for the identification of this species were thoroughly recorded using the scanning electron and stereo microscopes. Furthermore, DNA barcoding was used to confirm the morphological identification. The morphological examination identified the species as Heterocypris salina, where it revealed an accurate description for its carapace, valves and appendages. However, few dissimilarities with the description of that species by other authors were noted. The sequencing of partial sequences of 28S, 18S rRNA genes confirmed the results of the morphological identification. New barcodes for 28S, 18S rRNA genes and cytochrome oxidase subunit 1, COI gene, of H. salina were added to GenBank databases. Based on morphological and genetic evidences, this study adds new species to the biodiversity inventory of the aquatic environment of Egypt. Furthermore, COI sequence for Heterocypris salina has been submitted on the GenBank databases for the first time to be used as a marker for identification of such species in the future.