Using ecological, taxonomic and phylogenetic approaches, we here describe geographically isolated symbiotic relationships between a gobiid fish and two misdescribed alpheid snapping shrimps. This was discovered in the southwestern province of the Persian Gulf, more specifically, in the harsh hyperarid intertidal zone separating the coastal ecosystem from the Middle East desert. Phylogenetic results based on the 16S rRNA gene indicate the existence of two new cryptic species within the Alpheus lobidens De Haan, 1849 species complex, described and named here as Alpheus qatari n. sp. and Alpheus arabicus n. sp. Furthermore, phylogeographic results suggest resurrection of Alpheus crassimanus Heller, 1865 within the same species complex. A phylogenetic comparison of the endemic Arabic goby Cryptocentroides arabicus (Gmelin, 1789) with some of its congeners confirms its presence along both sides of the Persian Gulf. Ecologically noteworthy is the facultative symbiotic interaction between this endemic Arabic goby with the two mentioned endemic alpheid shrimps within two distinct ecosystems. Therefore, we herewith report a case of exceptional symbiosis of a littoral fish species with two potential partners, niche-restricted to shallow intertidal zones, however, with niche differentiation defined by the adaptability of each associated shrimp species. Furthermore, the presence of the goby depends on suitable sediment needed for burrowing: either gravel in the periphery of coral reefs, or mud in the periphery of mangrove ecosystems. The corresponding ecology, taxonomic status and phylogeography are discussed with respect to the recorded facultative character of the symbiotic relationship.