This study evaluated the prevalence and molecular traits of Babesia bigemina and Babesia bovis in cattle and water buffaloes from two regions in Colombia over three sampling periods. The researchers found an overall molecular prevalence of 31.6% for B. bigemina and 14.4% for B. bovis in cattle, and 23.6% for B. bigemina and 17.7% for B. bovis in buffaloes. Higher infection rates were seen in the wet and late wet seasons. Phylogenetic analysis revealed high genetic diversity among isolates with no clustering by host species. This longitudinal study provides new insights into the epidemiology of babesiosis in livestock in Colombia.