Microphytobenthic assemblages are fundamental components of shallow coastal marine environments, contributing significantly to primary production, nutrient cycling, and mediating biogeochemical interactions between sediments and water column. Although all microalgal classes are represented in these communities, diatoms (Bacillariophyceae) are the most dominant. Epiphytic diatoms, in particular, are able to colonize the leaf surfaces of marine seagrasses, forming highly dynamic habitats. Despite their high productivity and recognized sensitivity to environmental changes, these communities are frequently underrepresented in ecological monitoring efforts. Studying them is particularly crucial for understanding ecosystem stability and response to stress in extreme and sensitive regions like the Arabian Gulf, known for high salinity, high temperatures, and increasing anthropogenic pressure. This study explores the diversity and relative abundance of epiphytic diatom communities associated with three seagrass species (Halodule uninervis, Halophila stipulacea, and Halophila ovalis) along the Saudi Arabian coast of the Arabian Gulf, with sampling conducted during both winter and summer seasons. Through scanning electron microscopy (SEM), we identified dominant taxa and evaluated seasonal and spatial variation in assemblage composition. Diatoms were confirmed as the most abundant epiphytic group, with the genus Cocconeis comprising 96.2% of total diatom abundance and represented by four major species. During the winter, the highest abundance was observed at the central sampling site, while in summer, it peaked in the northern location. Halodule uninervis showed higher abundance of epiphytic diatoms in winter, while Halophila ovalis was the most colonized during summer. The composition of the diatom communities was predominantly influenced by seasonal variation, whereas site-specific differences had a limited impact. These findings enhance our understanding of diatom-seagrass associations, particularly in extreme environments such as the Arabian Gulf, and underscore their potential value as bioindicators in future monitoring programs.