A small Prorocentrum species was found during a pilot taxonomic survey of marine benthic dinoflagellates in the northwestern Arabian Sea, Oman. Based on the study of cells from natural samples and laboratory cultures using light and scanning electron microscopy, this taxon is attributed to the little-known Prorocentrum sipadanense, recorded so far only from East Malaysia. The description of this species has been emended to include details of internal cell structure, composition of its periflagellar area and intraspecific variability in size, shape and pore pattern. Round to oval or ovoid cells of P. sipadanese are surrounded by a prominent marginal ridge and are 17.9–23.9 µm long and 15.0–19.8 µm wide, with a foveate to reticulate thecal plate surface and asymmetric and scarce pore pattern. The small, V-shaped periflagellar area is composed of nine platelets. Cells possess two golden-brown chloroplasts with a central starch-sheathed pyrenoid and small posterior nucleus. In addition, the phylogenetic position of this taxon in Prorocentrum was revealed for the first time based on SSU and LSU rDNA data. The presence of P. sipadanense among epiphytic dinoflagellates from the Omani coast constitutes its first report from the Indian Ocean.