The native fishes of the Great Lakes basin consist of 153 species, 64 genera, and 25 families. The total ichthyofaunal lists for the several lakes and (in parentheses) their tributary basins are as follows: Nipigon (and tributaries), 40; Superior, 53 (82); Michigan, 91 (135); Huron, 90 (112); St. Clair and Detroit River 108; Erie, 106 (125); Ontario, 95 (125). (These totals include 21 introduced species, most named species of ciscoes and chubs, and the blue pike (Stizostedion vitreum glaucum).)Several areas show notable within-species differentiation. Tributaries to Lake Ontario are part of a zone of secondary contact of a few small, nonmanaged, subspecies that entered the basin from both eastern and western glacial refugia. In the Great Lakes themselves, stocks of lake trout (Salvelinus namaycush), ciscoes, walleyes (Stizostedion vitreum vitreum), and a few nonmanaged species stem from differentiation within the basin or reflect interglacial events that occurred in Mississippi refugia.Species distribution patterns suggest colonization of the Great Lakes by 122 kinds solely from Mississippi basin refugia, 14 kinds only from Atlantic drainage refugia, and dual refugia for at least 18 kinds. Geological evidence provides some support for this interpretation. It is unlikely that any species colonized the Great Lakes from an Alaskan refuge in the past 14 000 yr.The ciscoes and chubs of the genus Coregonus include numerous genetically differentiated stocks, some of which may predate the opening of the Great Lakes in the past 14 000 yr. This conclusion is based on the occurrence in Lake Nipigon and Lake Superior of several forms that must have colonized prior to 9000 yr ago when the last access existed from Lake Superior to Lake Nipigon. At least four and perhaps up to eight forms of Great Lakes coregonines probably survived (or differentiated during) the last glaciation south of the ice in proglacial waters at the heads of major river systems. There is no evidence to support the hypothesized post-Wisconsinan dispersal of any of these forms from a northwestern refugium or their Pleistocene derivation by introgression with a Eurasian species.Despite the evidence for some long-standing genetic differentiation within Coregonus, morphological and biochemical characters fail to support the unequivocal recognition within the Great Lakes of more than one to four current biological species (apart from clupeaformis). The presently recognized species are groups of stocks whose position in the classification system is problematical. The named groups (two of which are extinct) included numerous stocks that were (or are) isolated by homing behavior specific to time and place. The lack of intrinsic reproductive isolation among forms increases their vulnerability to extinction because rare forms apparently hybridize with common forms spawning at adjacent times or places.Key words: biogeography, Coregonus, fish, Great Lakes, introduced fishes, Pleistocene, species, subspecies