This algological study was carried out during the duration from January to March, 2019 on the patterns of benthic microalgal species distribution and diversity and the community composition of the identified species that attached on artificial glass slides substrate in Embikhah Khor. On the basis of possible influence of land activities, four sampling stations were preselected to represent the khor area. As a result, 46 identified species from 27 genera under 18 families and 4 divisions were classified. The diatoms were the most diverse group with 31 species followed by the dinoflagellates (7), blue green algae (5) and green algae (3). The combination of these assemblages characterized by higher alpha species diversity and richness growth of diatoms. Higher significant (p < 0.05) ratio of pennate benthic diatoms compared to centric forms was recorded. The diatomic species which were the pioneering community of early ecological succession development indicated the relatively pristine nature of Embikhah Khor ecosystem. The gradual decrease in α- species diversity from station 4 to station 1 was inconsistent with organic load in each station. Strong positive correlation between beta diversity and turnover ratio was observed. Meanwhile, there was strong positive correlation (r2= 0.8393) between alpha and beta diversity. Gamma diversity value which is influenced by alpha and beta diversity values was 26 taxa. Analysis of station similarity of community composition separated several clusters of stations at the different similarity level (71-86%). Amongst species composition, twenty of the record species were potentially harmful species, all of them found in low species diversity except Navicula spp, Nitzschia spp and Peridinium spp. Around 44% of alpha species diversity index covered byharmful microalgal species. Nevertheless, no harmful blooms have been reported or expected to appear in Embikhah Khor.