<p>Bitterling fishes spawn in the gills of freshwater mussels and the mussels infect their larva (glochidia) to host fish for development and dispersal. The relationship between bitterlings and mussels has thus been considered a ‘mutualistic symbiosis’, although this notion remains controversial. Freshwater mussel populations have severely declined recently worldwide, due to increasing anthropogenic pressures, which can pose large threats to the bitterling’s local extinction. We analysed and compared genetic diversity and phylogeographic/population structure of the endangered bitterling (<i>Tanakia signifer</i>) and its symbiotic mussel (<i>Nodularia breviconcha</i>) at 16 localities in the Han River using mitochondrial DNA variation. The results of haplotype network and demographic analyses showed that the two species exhibited shared phylogeographic patterns – a recent sudden population expansion suggested by a star-like shallow genealogy. The overall concordance in the phylogeographic/population structure between <i>T. signifer</i> and <i>N. breviconcha</i> may result from their co-evolutionary symbiotic interaction, the common geographical setting, or a combination of both. A significant positive correlation in levels of population differentiation between the two species may provide some evidence supporting their close symbiotic relationship. However, further analyses with more molecular markers and more samples will be needed to disentangle the effects of geography and co-evolutionary processes. The South Han River populations had lower genetic diversity than Imjin-Hantan and North Han Rivers for both species, which may indicate a need for increased conservation efforts. The findings of this study will provide insight into the conservation implications for the endangered bitterling fish and also co-occurring its symbiotic Korean endemic mussel species.</p>