Stable isotope ratio measurements of fish remains from archaeological sites are relatively rare so here we report results of 201 fish remains from two Bronze and Iron Age sites along the Syrian (Tell Tweini) and Lebanese (Sidon) coast to document the inter- and intra-specific variation of the δ13C and δ15N isotope values. Due to poor preservation, successful isotopic results were only obtained from 42 specimens (21%). Our results were combined with previously published fish isotopic results from Sidon (n = 16) so that a total 58 specimens representing 16 different fish taxa are presented. A wide variation was observed between species that appears to be related to the ecology of the fish, in particular their salinity tolerance and feeding behaviour. The largest intra-specific variation was observed in mullets (Mugilidae) and seabreams (Sparidae) in both δ13C and δ15N values, and it appears, after comparison with published data from the Northern Aegean, some clustering occurs with location. However, the data clustering is not discrete enough to allow provenancing of fish remains from archaeological sites in this region. This large series of fish isotope values can also serve as an isotopic baseline for other studies, including the dietary reconstruction of Eastern Mediterranean human remains.