To conduct comparative epidemiology of parasitologically positive (patent) and polymerase chain reaction positive (latent) cases of bovine babesiosis in Bet Region (low-lying areas adjoining Sutlej, Beas, Ravi, and Ghaggar rivers of Punjab) of diverse agroclimatic zones of Punjab state in relation to haematobiochemical parameters as patho-physiological markers, blood samples from 783 dairy animals (487 buffaloes and 296 cattle) were analysed parasitologically by Giemsa-stained blood smears (GSBS) and by molecular-based polymerase chain reaction (PCR) targeting SpeI-AvaI restriction fragment of Babesia bigemina. We ruled out the endemicity of the disease with 2.17% patent and 3.96% latent cases of B. bigemina with significantly higher prevalence (P < 0.01) in cattle than buffaloes. The spatial distribution for a guideline to local veterinary practitioners and policy-makers indicated highest number of patent and latent cases in western zone and undulating plain zone, respectively. District wise highest prevalence of patent as well as latent infection observed in SBS Nagar of undulating plain zone showed substantial agreement (Kappa value: 0.70) between the two techniques. Haematology revealed marked microcytic hyperchromic anaemia in patent animals of group I (GSBS positive; n = 17) and latent animals of group II (PCR positive; n = 14) as compared to disease-free controls (group III; n = 10). Blood urea nitrogen (BUN), creatinine and gamma-glutamyltransferase (GGT) levels were significantly increased (P < 0.05) in group I in comparison to group II and group III indicated comparative pathogenic effect of babesiosis in patent cases. Though patent cases showed higher pathogenicity of babesiosis, diagnosis of latent infection is significant as it may act as source of infection for spread to other highly prone bovines.