Zoantharians are one of the least studied orders of benthic cnidarians of the Persian Gulf. A survey and molecular analysis was conducted to determine zoantharian species diversity in the Persian Gulf. For this purpose, 63 colonies of zoantharians were collected from Hengam and Larak Islands in the Strait of Hormuz and some morphological characteristics of each specimen were recorded, i.e. sand encrustation, polyp shape and colour, oral groove, oral zone and oral disc colours as well as tentacle number and colour. After DNA extraction, mitochondrial 16S ribosomal DNA (16S rDNA) and cytochrome oxidase subunit I (COI) were amplified by polymerase chain reaction (PCR). Based on obtained 16S rDNA and COI gene sequences, five putative species-level clades were identified: Zoanthus sansibaricus (N = 30), Palythoa tuberculosa (N = 12), Palythoa mutuki (N = 2), Palythoa aff. mutuki (N = 18) and Neozoanthus sp. Iran (N = 1). While the first three are known species, the last two were potentially novel undescribed species. Palythoa aff. mutuki has an external appearance similar to Palythoa mutuki. However, mitochondrial DNA sequences obtained from these specimens placed them in a previously undescribed species group. The Neozoanthus specimen was morphologically and molecularly different from other described Neozoanthus species. This is the first record of this genus from the Persian Gulf and neighbouring areas. Since there is not much work on zoantharians identification in the Persian Gulf, further sampling and investigation is needed to speculate on the accuracy of these potentially new species and to complete the knowledge of zoantharian diversity in this area.