Tilapia is reportedly affected by two RNA viruses; tilapia lake virus (TiLV) and nervous necrosis virus (NNV), both causing up to 90% mortality in acute infections. Random investigation was performed with samples from 4 farms located in the department (province) of San Martín, a region with the highest concentrated tilapia farms in Peru. Fish tissues of the eyes, brain, and liver were subjected to molecular detection and histopathological examination. The results showed that all of the samples were tested negative for NNV but 4 samples from 3 farms were TiLV positive. Syncytial hepatitis lesion typically found in TiLV-infected tilapia was also observed. TiLV genome sequence analysis of the Peruvian isolate showed 96.89–97.13% and 95.38–95.68% identity to that of the Israeli and Thai isolates, respectively. Multilocus sequence phylogenetic analysis based on 8305 nucleotides of five TiLV isolates indicated that the Peruvian isolate is genetically close to the Israeli isolates, possibly suggesting the same origin. © 2019 Elsevier B.V.