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Background  Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon ( Oncorhynchus nerka ), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria,  Flavobacterium spp ., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit ( AtpA ) within the genus  Flavobacterium.  Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of  Flavobacterium AtpA  amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat.    Results  We identified 10  Flavobacterium AtpA  haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as  F. psychrophilum  were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of  Flavobacterium AtpA  amplicons between samples from the different spawning habitats.    Conclusions  We confirmed the presence of  Flavobacterium spp.  in both spawning habitats and found weak evidence for increased  Flavobacterium  diversity in kokanee sampled from stream-spawning sites. However, the quantity of  Flavobacterium  DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with environmental sampling to better understand the ecology of pathogen infection in this species.    Electronic supplementary material  The online version of this article (doi:10.1186/1756-0500-7-778) contains supplementary material, which is available to authorized users.

Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon