Small ruminant lentiviruses (SRLVs) cause a persistent, chronic degenerative, multisystem disease in goats and sheep. This study was performed to assess the genetic distribution of SRLV in Mexico and the risk factors that favor its presence in sheep and goats across different production units. In total, 890 goats and sheep (383 and 507, respectively) from 52 mixed-species and single-species flocks in the northern, central, and southern regions of Mexico were analyzed. Serological and molecular diagnoses were conducted. PCR-positive samples were further analyzed via real-time PCR to identify genotypes A and B. The survey data were evaluated to determine the relationship between virus presence, seropositivity, and associated factors in the flocks. Of the 890 animals sampled (507 sheep and 383 goats), 40% (354/890) tested positive for antibodies specific for SRLV (229 goats and 125 sheep), while 78% (697/890) were positive for the viral genome (340 goats and 357 sheep). The results confirmed that genotype A circulated in 15% of infected animals, genotype B circulated in 66%, and 19% were co-infected with both genotypes. This study highlights the circulation and spread of SRLV genotypes A and B in goat and sheep flocks in Mexico. The risk factors that showed a significant association with seropositivity were age, flock size, and veterinary assistance. For molecular positivity detection, production with mixed flocks was added as a variable in the central region cluster, in addition to the variable knowledge of SRLV diseases and contact with other flocks in the sheep cluster. Other factors such as species cohabitation, cleanliness, and preventive measures were associated with the presence of clinical signs.