Abstract The infections caused by feline leukemia (FeLV) and feline immunodeficiency (FIV) viruses, are relevant in Feline Medicine due to the severe complications of the disease and related pathologies in domestic cats. This study describes clinical findings related to FeLV and FIV, regressive FeLV infections and identification of prevalent FeLV genotypes in domestic cats from Mérida, Yucatán, México. Hundred domestic cats with clinical manifestations of diseases associated with feline retrovirus infection in veterinary centers in Mérida, were submitted to a general physical examination, venipuncture to collect blood, and a quantitative hemogram. Detection of antigen (FeLV) and antibody (FIV) was used to estimate infection frequency. The percentage of regressive FeLV infections was determined by PCR of an env gene segment. Some FeLV amplified products were sequenced with the Sanger method and used to construct a phylogenetic tree. The predominant FeLV and FIV clinical infection findings were gingivitis, gingivostomatitis, periodontal disease and anemia. We found a 10% infection frequency for FeLV by antigen detection, and 17% for FIV by antibodies detection. PCR frequency detection for FeLV was 58%, and 52% were regressive infections. The phylogenetic analysis identified sequences associated with FeLV-A, and endogenous or recombinant FeLV that had not previously been identified in México. The frequency of infection by both retroviruses was higher in Mérida, Yucatán, than those described in previous studies. Cats with FeLV predominantly had regressive infections, but the role that endogenous or recombinant retroviruses play in disease development remains unknown.