We conducted surveillance for flavivirus infection in peridomestic rodents in Merida, Mexico in 2011–12. We captured 161 rodents inside private residences, using Sherman traps, including 86 house mice (Mus musculus) and 75 black rats (Rattus rattus). Serum from each animal was assayed by plaque reduction neutralization test (PRNT) using two vertebrate-specific flaviviruses (Apoi and Modoc viruses) and five mosquito-borne flaviviruses (dengue 2, dengue 4, St. Louis encephalitis virus, West Nile, and yellow fever viruses). Sixty-one (37.9%) rodents had antibodies that neutralized at least one virus. Prevalences for flaviviruses were 64.0% and 15.1% for black rats and house mice, respectively. None of the PRNT₉₀ titers exceeded 80, and often they were highest for Modoc virus. These data suggest that a subset of rodents had been infected with Modoc virus or a closely related flavivirus that was not included in the PRNT analysis.