The abundance and vertical distribution of microcopepods sampled by nets with 55 μm mesh size was compared for two neighbouring but hydrographically different areas, the Gulf of Aqaba and the northernmost Red Sea, during spring 1999. The vertical structure of the total microcopepod communities differed considerably between the two regimes: In the stratified waters of the Red Sea, calanoids outnumbered oncaeids as well as oithonids at 0–100 m, whereas oncaeids dominated in all meso- and bathypelagic layers below 100 m deep. In the unusually deep vertically mixed waters of the Gulf of Aqaba, calanoids outnumbered each of the non-calanoid taxa as deep as 250 or 350 m, whereas the oncaeid dominated deep water community was restricted to depth ranges below 400 m. Dominant non-calanoid species in both areas were Oncaea bispinosa, Paroithona pacifica, Oithona simplex, Spinoncaea ivlevi, O. tregoubovi and O. cristata. O. scottodicarloi occurred in exceptionally high numbers in the northern Gulf. Pronounced differences between the two areas were found in the vertical distribution of poecilostomatoid species. By comparing the present results with published data from the central and southern Red Sea and other tropical and warm-temperate oceanic areas, intra- and inter-oceanic differences in the structure of microcopepod communities in oligotrophic areas are discussed. The high abundance and vertically extended range of calanoid copepods during spring appears to be a specific feature of the Gulf of Aqaba, indicating an unusual vertical succession in the trophodynamic structure of the copepod fauna in this area.