The four species that comprise the Bufo boreas group of toads are critically imperiled in all or portions of their geographical ranges. We present data from 16 microsatellite loci isolated from B. boreas that cross‐amplify in these four species. These markers have proven useful in the analyses of population structure and conservation genetics, and provide a powerful tool for future researchers who seek to understand the conservation genetics of these rare toad species. Polymorphism was assessed for 339 individuals from seven populations representing the four species. All loci were polymorphic (X̄ = 8, range of four to 19 alleles). Three loci were not in Hardy–Weinberg equilibrium (HWE) in one population, and one of these loci was out of HWE in a second population (P < 0.003 after Bonferroni correction for multiple tests). However, there were no systematic deviations from HWE across all study populations. Small populations in fragmented habitat appear to explain the existing HWE deviations.