In a focused analysis of Prochlorococcus population structure in the western North Atlantic, we found that the relative abundances of ecotypes varied significantly with depth and, at seasonally stratified locations, with degree of vertical mixing. More limited regional variation was observed ( e. g., Sargasso Sea, Gulf Stream, continental slope, and equatorial current), and local patchiness was minimal. Modeling of a combined North and South Atlantic data set revealed significant, independent effects of light and temperature on ecotype abundances, suggesting that they are key ecological determinants that establish the different habitat ranges of the physiologically and genetically distinct ecotypes. This was in sharp contrast with the genus Synechococcus, whose total abundance was related to light but did not vary in a predictable way with temperature. Comparisons of field abundances with growth characteristics of cultured isolates ofProchlorococcus suggested the presence of ecotype-specific thermal and light adaptations that could be responsible for the distinct distribution patterns of the four dominant ecotypes. Significantly, we discovered that one "low-light-adapted" ecotype, eNATL2A, can thrive in deeply mixed surface layers, whereas another, eMIT9313, cannot, even though they have the same growth optimum for ( low) light.