This study investigates for the first time the fish communities of shallow water habitats along the Jordanian coast. Transects of 50 m length were marked at six sites along the Jordanian coast. At each site visual censuses were conducted along three transects at 6 m respectively 12 m depth. In this study 202 species belonging to 123 genera and 43 families were identified. Most individuals belong to the families Serranidae, subfamily Anthininae (37.1%), Pomacentridae (22.3%) and Labridae (8.0%). The most abundant species are Pseudanthias squamipinnis (36.8 %), Pomacentrus trichourus  (6.0 %), Atherinomorus lacunosus (5.1 %) and Paracheilinus octotaenia (3.7 %). Multivariate analysis of the data is based on Bray–Curtis similarities. Cluster analysis of the sites shows three main clusters: the seagrass dominated Al Mamlah Bay and the 6 m and 12 m transects of the coral dominated sites. This indicates different fish communities at 6 and 12 m depth as well as in the seagrass dominated Al Mamlah Bay. Confirmation of this pattern is evidenced by an ANOSIM significance test. This picture can be connected to the benthic substrate. Cluster analysis of the benthic habitat composition gives the same pattern. Analysis by species shows two main clusters, one representing fishes of the coral habitat, the other fishes of the seagrass beds. A biogeographic comparison based on presence/absence of species showed decreasing similarity of fish communities from the northern tip of the Gulf of Aqaba going south through the Red Sea proper into the Indian Ocean.