Small pelagic fishes particularly anchovy (Encrasicholina punctifer) and sardine (Sardinella sindensis) have an important role to support the Iranian fisheries and are distributed along the coastal waters of the Persian Gulf and Oman Sea. Using a logbook on small pelagic fisheries, a GIS-based environmental modeling approach was applied to investigate the presence and abundance of anchovy and sardine in relation to environmental variables. Redundancy analysis (RDA) was applied to provide a preliminary view of the relationships between fish presence/absence and environmental variables. Generalized Additive Models (GAMs) indicated the presence/absence of fish was related to distance from the nearest coast, depth, sea surface Chlorophyll-a, and SST. Results of the EFH showed that sardine is concentrated in specific areas of more favorable conditions, such as north of the Persian Gulf and all areas of the northwest of the Oman Sea. However, EFH of anchovy showed a more widespread distribution, occupying most of the north-west of the Oman Sea coastal waters, south of Qeshm Island in the Strait of Hormoz as well as the Parsian district in the north of the Persian Gulf. In this study, it seems that the anchovy showed the probability of presence in the areas with more distance from the coastal waters. However, the EFH probability presences of sardine were predicted for near coastal water and obviously, shallower waters. Due to the development of small pelagic fisheries, it is highly recommended to investigate anchovy and sardine fishing possibility in areas with high EFH prediction probability.