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Peromyscus bolyii is a dominant species in rodent communities in southwestern New Mexico and is a known carrier of Limestone Canyon virus (LSCV) in Arizona. Five species of Peromyscus were collected from Hidalgo and Grant County, most of which were P. boylii. All mice were serologically tested for antibodies to Sin Nombre virus and Rio Mamore virus. Lung tissue from all seropositive and negative mice was used for RNA extraction, amplification, and sequencing using newly designed primers specific to LSCV for both the S and M segments. A phylogenetic analysis of the virus was performed and showed a about a 5.5% divergence from LSCV in Arizona, and a 4.5% divergence among P. boylii representing two clades found in southwestern New Mexico. Also, viral RNA was obtained from a seronegative mouse emphasizing the importance of PCR testing in addition to serology testing to determine the presence of hantaviruses.