Elucidation of the sex determination (SD) mechanism in the Flathead grey mullet (Mugil cephalus) is required for exploiting its economic potential by production of mono-sex progeny. The objective of the current study is to construct a first generation linkage map of the Flathead grey mullet with emphasis on detection and characterization of its sex determination region. The mapping family (n=48) consisted of full-sib progeny that were validated by genotyping of 9 microsatellite genetic markers. The deep sequencing data of a single male from the mapping family was assembled and aligned to the Nile tilapia (Oreochromis niloticus) genome.