The number of goatfish sp­­ecies has increased recently, thanks in part to the application of molecular approaches to the taxonomy of a family with conservative morphology and widespread intraspecific color variation. A new subspecies Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall subsp. n. is described from the Red Sea and Arabian Sea, including Socotra and Gulf of Oman. The two subspecies are distinguished by 1.7% sequence divergence at the mitochondrial cytochrome b gene, a yellow caudal fin, 25-28 gill rakers, and 37-38 lateral-line scales. The morphometric examination of specimens of M. flavolineatus flavolineatus revealed variation in head length, eye diameter, and barbel length, in western direction from the Hawaiian Islands, South Pacific, Micronesia, and the East Indies to the Indian Ocean.  The population of the subspecies in the Gulf of Aqaba is distinguished from that of the remaining Red Sea by shorter barbels, smaller eyes, shorter heads, and shorter pelvic fins. We present a list of 26 endemic fishes from the Gulf of Aqaba and discuss and discuss the probable basis for the endemism in the light of the geological history of this region.