Macrobenthic communities in shallow mangrove-seagrass habitat at the southern portion of Saudi Arabia, Red Sea were explored to (i) characterize their diversity and abundance; (ii) examine the variability among outer, middle and inner stations; and (iii) evaluate the catch performance of scoop (bulldozer) and Van Veen grab. Fifteen sampling collections (9 scoop and 6 grab) captured 4,491 individuals encompassing 18 taxonomic groups. Polychaetes predominated the samples, followed by pelecypods, gammarids, gastropods, and isopods. The species richness did not differ among stations. The density of macrobenthos was significantly (ANOVA, F = 5.51, p = 0.020) higher in the outer and middle stations than the inner station. Moreover, the difference of macrobenthos abundance was seemingly associated with the sediment type and the presence and absence of seagrass. The proportion of non-shared groups over the total number of groups increases from the outer to the inner stations (30.7 to 57.1%), which revealed a degree of difference in the community. The exclusive presence of stomatopods in the inner station suggests their territorial behavior. As well, Van Veen grab captured higher taxonomic groups than scoop; the difference in abundance was not significant. Grab was more pragmatic with ease to operate and thus higher catch efficiency.