Two independent sampling methods were used to collect genetic samples from grizzly bears (Ursus arctos): (i) hair traps—corrals of barbed wire with lure in the center systematically distributed using an 8 x 8 km (1998, 2000) or 7 x 7 km (2004) grid and (ii) bear rubs—naturally occurring trees or other objects that bears rub on fitted with barbed wire (1998–2000, 2004, and 2009–2012). From 1998 to 2000, sampling occurred on 8000 km2 in the northern extent of the Northern Continental Divide Ecosystem (NCDE), whereas systematic and consistent, ecosystem-wide sampling occurred in 2004 and 2009–2012. In total, there were 6160 confirmed grizzly bear detections, leading to the identification of 1115 unique individual genotypes (520 male, 595 female). The data contain the genotypes or partial genotypes of those 1115 individuals, with an individual ID, sex, and up to 24 genotyped, codominant loci. The loci represented are; G10J, G1A, G10B, G1D, G10H, G10M, G10P, G10C, CXX110, CXX20, G10L, MU50, MU59, G10U, MU23, G10X, REN145.P07, MSUT2, CPH9, MU51, REN144.A06, MU26, D123, D1A. Each locus is split into two columns, the first of which contains the first allele and the second of which contains the second allele of each genotyped locus for each individual. Values within the columns of each locus represent the size of the alleles.