The shortfin lizardfish Saurida micropectoralis is recorded here for the first time from Jizan, Southern Red Sea, based on morphological and molecular analyses. This species closely resembles both S. tumbil and S. lessepsianus. However, S. micropectoralis is characterized by translucent whitish pelvic fins (vs. dusky in S. tumbil), indistinct blackish spots on the upper margin of the caudal fin (vs. distinct black spots (6–8) in S. lessepsianus), a short pectoral fin that never reaches the origin of the pelvic fin (vs. reaching a little beyond the base of the pelvic fin in S. lessepsianus), three rows of teeth on the outer palatines (vs. two rows in S. lessepsianus) and a pale whitish stomach and intestine (vs. greyish or black anteriorly in S. lessepsianus). Molecular analyses based on COI haplotypes confirmed the species-level identification but also revealed the existence of four distinct lineages across the species distribution range. The COI data revealed a clear geographic partitioning of haplotypes, indicating restricted gene flow and suggesting the presence of four cryptic species or, at minimum, independent evolving evolutionary units within Saurida micropectoralis. Populations of the shortfin lizardfish are well established in the Southern Red Sea and belong to a genetic lineage reported along the East African coast (Madagascar, Mozambique and Tanzania) and India.