This study examined the diversity of siderophore-producing bacteria in the intestinal tracts of coastal fish in Japan and screened candidate bacterial strains for probiotic use in aquaculture. Of the 2637 bacteria isolated from the 27 fish specimens (13 species) and six environmental samples collected in this study, 266 isolates exhibited the ability to produce siderophores. Siderophore producers were detected in the intestines of 18 of the fish specimens caught (68%) at densities of 2.3 × 104–2.3 × 108 CFU g−1, in all three seawater samples at 2.0 × 102–1.3 × 103 CFU mL−1 and in all three sand samples at 2.6 × 101–2.8 × 104 CFU g−1. These findings suggest that siderophore-producing bacteria are widely distributed in the intestinal tracts of coastal fish and their environments. Analysis of 16S rRNA gene sequences revealed that the siderophore producers belonged to 38 species, of which Vibrio splendidus, Vibrio ichthyoenteri and Vibrio crassostreae accounted for 32.7%, 19.5% and 11.3% of the 266 isolates, respectively, suggesting that these bacteria are indigenous to the intestinal tract of coastal fish. Six bacterial species, Enterovibri norvegicus, Photobacterium leiognathi, Photobacterium phosphoreum, Photobacterium rosenbergii, V. crassostrea and Vibrio scophthalmi were identified as possible candidates for use as probionts in fish aquaculture.