Wildlife conservation and management efforts often rely on accurate differentiation of morphologically similar taxa. While effective management of a single taxon is dependent on accurate harvest estimates, subtle morphological differences can make subspecies determination error-prone and time consuming for even experienced field biologists. Here we demonstrate that genetic approaches to identification can provide accurate subspecies typing results while remaining cost effective. The Tule Goose (Anser albifrons elgasi) is a demographically vulnerable subspecies of the Greater White-fronted Goose (A. albifrons, GWFG), that overwinters in the Sacramento Valley and Bay-Delta regions of California alongside the more abundant Pacific GWFG (A. a. sponsa). This sympatry creates a management challenge for estimating and limiting seasonal Tule Goose harvest. Using a panel of 83 single nucleotide polymorphisms (SNP) we can efficiently and accurately distinguish Tule Geese from Pacific GWFG from samples easily obtained at hunter check stations. SNP genotypes show clear differentiation through principal component analysis and estimation of STRUCTURE ancestry coefficients. Multi-year analyses suggest Tule Geese typically average 5% of the GWFG harvest at designated check stations. Yet during 2021-2022 drought conditions, genetic typing discovered Tule Goose harvest increased to 29% of GWFG harvest, providing robust support for the management decision to limit duration of the hunting season.