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Accurate sex identification of prey remains can provide valuable insights into selective predation, but field studies are often constrained by degraded or digested material. We developed and validated a molecular sexing protocol for the Brown lemming (Lemmus trimucronatus), a keystone prey species in the Canadian High Arctic. Using tissues from known-sex individuals, we tested candidate primers and established a multiplex PCR combining sex-chromosomal zinc-finger genes (ZFX and ZFY) and sex-determining region Y protein (SRY) markers. This method reliably distinguished males and females, with 98% concordance between genetic and morphological sexing. Validation included dentary bones subjected to artificial digestion, demonstrating consistent success regardless of tissue type or degradation treatment. We then applied the protocol to field-collected lemming remains from snowy owl pellets, ermine caches, and predated lemming winter nests. Despite variable preservation and exposure conditions, 87% of samples yielded viable results, with soft tissues achieving highest success rates and bones and teeth remaining suitable DNA sources even after digestion. Our results confirm that molecular sexing of lemmings from predator-derived remains is feasible, accurate, and robust to sample quality. This protocol can enable researchers in Arctic ecosystems to analyze sex-specific predation patterns even when direct observation or fresh tissue sampling is impractical.