A sequence analysis is described of a fosmid clone from a coastal marine metagenomic library that contains a 16S rRNA gene with high sequence similarity to that of the SAR11 bacterium 'Candidatus Pelagibacter ubique' HTCC1062. The sequence of the fosmid clone was 32 086 bp in length and contained 23 187 bp of the 48-kb hyper-variable region 2 (HVR2) present in the genome of 'Cand. P. ubique'. However, half of the sequences within the HVR2 region of the fosmid clone show little sequence similarity to or have no representative homologues in the genome sequence of 'Cand. P. ubique' HTCC1062. Given their putative functions, the acquisition of these genes suggests that SAR11 could harbour more diverse phenotypes than represented by the 16S rRNA taxonomy. Variation in SAR11 genomes from different locations might explain why SAR11 is abundant in so many diverse marine provinces.