Seven species of ciscoes (Coregonus, subgenus Leucichthys) were found in the Great Lakes as recently as the early 1950's. Variation within and among species of Great Lakes ciscoes indicates that much of the divergence occurred within lakes. Following postglacial colonization by perhaps two or three species, population differentiation began with homing and reproduction at different localities and times. Physiological interaction between temperature (depth) and maturation time, as well as behavioral tendencies to home to spawning grounds and mate with related individuals, are the basis of premating reproductive separation. Phenotypic differences between populations indicate that ecological character displacement has been an important mechanism in the divergence. Introgression has obscured morphological species boundaries at the same time as intralacustrine speciation has created local subgroups, providing an unresolvable conflict between species definitions based on morphological and other characters and definitions dominated by inferred reproductive isolation. Species should be considered as the smallest diagnosable units within a phylogenetic framework, in which diagnoses are strictly by derived characters. Ecological and seasonal species could be recognized by application of a trinomial, equivalent to the subspecies trinomial.