Gamaridae is one of the most diversified and prominent family of Amphipoda. This order provides the main food for the most fish species and are so sensitive to environmental pollution, which leads to their ecological and economic importance. However, regarding to high degree in morphological and ecological differences among the different species of the order, the first step to study these group of animals is to identify the species. The main aim of this study was to collect and identify Gammarus species distributed in the rivers of the eastern part of Tehran Province, including Jajrood, Hablehrood and Lar. In order to collecting the samples, ten sampling points in different parts of three rivers were selected. Sampling was carried out seasonally from October 2013 to June 2014. 20 samples were taken from each point by dredge device and kept in ethanol to transfer to the laboratory for further experiments. For identification the samples to species level, some of the available classification keys were applied. The samples were identified by classification key at species level and results showed that all of samples were G. komareki. Then, molecular assessments by DNA extraction, DNA qualification and isolation the mitochondrial gene in COI segment by using universal primers were conducted; at the end of the process was finished by gene sequencing. The obtained sequence was compared by Genbank. The results showed that G. komareki has varied populations in the rivers of eastern part of Tehran province. Although there was no significant morphological difference among the populations, their different abundance revealed the difference in the rivers environments.