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Along the Mediterranean coast of Israel, two near-shore dolphin species are prevalent; <i>Tursiops truncatus</i> (least concern, IUCN) and <i>Delphinus delphis</i> (endangered, IUCN). Ship-board surveys and sporadic sightings over the last two decades have shown that the two differ in distribution—<i>T. truncatus</i> is found along the entire coast and <i>D. delphis</i> only in the south. The environmental and anthropological factors affecting these species’ spatial distribution and determining their habitat preferences in this area are largely unknown. This work is a first attempt at summarizing 20 years of observations and studying habitat preferences for both species, by use of Generalized Additive Models. <i>T. truncatus</i> was found to be present in all areas of the continental shelf where survey effort coverage was sufficient, with a high affinity towards bottom trawlers. Model results showed <i>D. delphis</i> distribution to be associated to (shallow) water depths, though the factors driving their limited latitudinal distribution currently remain unknown. It is evident that <i>T. truncatus</i> and <i>D. delphis</i> are present in segregated areas of the Israeli continental shelf and <i>T. truncatus</i> currently sustains a delicate balance with continuously shifting human activities, while the drivers of <i>D</i>. <i>delphis</i> distribution are more specified, yet still not fully understood.