Bacterioplankton of the SAR11 clade dominate aquatic ecosystems but knowledge of their freshwater members remains limited due to a lack of cultured representatives. Here, we report the first isolate from the freshwater SAR11 subclade IIIb, a.k.a. LD12, obtained from surface waters in Lake Borgne, a lagoon on the southeastern coast of Louisiana. Consistent with pervasive ecological data, strain LSUCC0530 is highly restricted to growth at low salinities. Comparison of its distribution with the sister clade subclade IIIa, however, suggests that niche differentiation between sister taxa in coastal environments may be driven by more than salinity alone.