Abstract Infections with viruses of the Flavivirus genus were explored in 22 bats ( Artibeus jamaicensis ) from Merida, Yucatan, Mexico. The detection of the viral genus was performed by RT‐PCR, and infections with dengue (DENV 1–4), West Nile (WNV) and Zika (ZIKV) viruses were subsequently explored. Sequences from positive products were analysed using the BLAST algorithm to determine identity. In 7 (31.8%) and 2 (9.1%) bats, WNV and ZIKV were identified, respectively. The bioinformatic analysis showed 98%–100% coverage and identity for both viruses. Molecular evidence of WNV and ZIKV natural infection in bats from Yucatan, Mexico, is presented.