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In this stud, the diversity and abundance of benthic diatoms were evaluated in 9 stations located in Persian Gulf (Sirik) and Oman Sea (Gwatar, Abshirinkon) in winter and spring of 1394 -1395. Environmental factors including salinity, pH, aggregation and organic matter were evaluated. In this study, 72 species of diatoms belonging to 38 genera were identified. Abundance of diatoms in winter and spring were 23258 + 2961 and 16030 + 1206 per 100 g of sediment, respectively. Seasonal changes of biological indicators, Margalef, Shannon Parker, and Berger were 1.30 – 3.72, 1.28 – 2.89, 0.09 – 0.40, respectively. Based on two-way analysis of variance the abundance of diatoms was significantly different between stations (P > 0.05), but no significant differences were observed between two seasons (P > 0.05) based on t-test. There were positive correlations between grain size, salinity and organic matter with the diversity and abundance of diatoms. Station 9 in the Gwatar region with the highest percentage of silt-clay, organic matter and high salinity showed the highest diversity and abundance of diatoms in the sediment. The results showed that the diversity and abundance of benthic diatoms depend on grain size, organic matter and salinity.