Genuine freshwater fish faunas of 32 rivers in Fukuoka Prefecture, northern Kyushu, Japan, were surveyed between 1998 and 2005, in order to clarify their geographical distribution patterns. A total of 39 fish species/subspecies (10 families) were recorded in the field survey and from existing literature, a cluster analysis separating them into the Chikuzen-Chikugo and Chikuho-Buzen groups. The former was considered to include fauna influenced by mainland China and the Korean Peninsula, the latter being similar to the freshwater fish fauna of rivers flowing to the Seto Inland Sea. The freshwater fish species in Fukuoka were roughly divided into those that occurred in rivers regardless of river length and those that tended to be present in rivers exceeding a certain length. The genuine freshwater fish fauna in Fukuoka is considered to have evolved through geographical isolation and the restriction of river length.