Begomovirus genus is a member of Geminiviridae family, that have the most species in comperision of other viral genuses infecting plants. Begomoviruses are notorious pathogens infecting dicotyledonous plants globally and exclusively transmitted by an insect vector whitefly, Bemisia tabaci. Whiteflie is one of the most important and prevalent pests in the warm south and southeast provinces of Iran and infect cucurbits fields in Sistan and Baluchestan province with a widespread population, too. Begomoviruses are single-stranded circular DNA viruses and have a wide host range of plants. There are different reports of infectious Begomoviruses species from world that can cause damage in cucurbits. Sistan and Baluchestan province is located southeast of Iran and is the largest province as area in contrast of other provonces in Iran with about 11.4% of total area of country. Therefore, in order to identify the Begomoviruses species infecting cucurbits in southeast of Iran were done several surveys in different regions of Sistan and Baluchestan province involved Saravan, Iranshahr, Nikshahr, Sarbaz, Konarak, Chabahar, Zabol, Zahak, Hamoon, Hirmand, Nimroz and Zahedan. Sampling has been taken from different cucurbits, such as different kind of melons, watermelon and squash, in 2016-2017. Sample collection were done from plants that shown vein yellowing, stunting, chlorotic, mottling, deformation and severe reduction of fruit size and co-infection with whiteflies and were transformed to laboratory. Then, total DNA were exteracted. Inorder to identify Begomoviruses species, from specific primers, Gem-CP-V-5' and Gem-CP-V-3' detecting Begomovirus genus in cucurbits were used. The expected PCR products from CP gene, about 600 bp size, were done sequencing to identify infected species. The results of 16 sample sequencing from different regions of Sistan and Baluchestan province showed Watermelon chlorotic stunt virus, WmCSV was only the Begomovirus specie infecting cucurbits in southeast of Iran. Phylogenic sequencing analysis results of 16 WmCSV isolates in this research with MEGA 5 softeware classified them in two apart groups. There didn`t show any relationship between geographical source or host in this province. Probably, spread of isolates belongs these two groups were done by whiteflies in southeast of Iran. The results of sequencings in this research, will be used to design constructs inducing RNA silencing against isolates were classified in both two groups.