A total of 480 suspected blood samples were collected from cattle (n=254) and buffaloes (n=226) during the study period from September 2011 to December 2014 for determination of prevalence of haemoprotozoan parasites from South Western Gujarat (Junagadh). The conventional optical microscopy of Giemsa stained blood smears revealed that 37% of cattle and 38.93% of buffaloes were infected with haemoprotozoan parasites including Anaplasma marginale, Babesia bigemina, Trypanosoma evansi and Theileria annulata. The animals infected with haemoprotozoan diseases showed lower total erythrocyte count (TEC), haemoglobin (Hb), packed cell volume (PCV), mean corpuscular haemoglobin concentration (MCHC) and higher total leukocyte count (TLC) and mean corpuscular volume (MCV). Incidence of haemoprotozoan infection between the breeds differed significantly (P<0.05). Haemoprotozoan infections were recorded significantly higher (P<0.001) in monsoon season followed by summer and being lowest in winter season in cattle. Over all prevalence in female animals were higher than male counterparts. In both the species, over all higher prevalence of babesiosis was recorded in comparison to other haemoprotozoan diseases and the difference being statistically non-significant (p>0.05). The prevalence of B. bigemina in bovines was associated with various risk factors namely age, season and breed (p0.05). Sex wise females recorded apparently higher infection rates than males. The multivariate logistic regression models showed that the risk of babesiosis was significantly higher in rainy season (OR=5.18, P=0.003) followed by summer (OR=3.9, P=0.019) compared to winter season. Conversely, in buffaloes, the risk of babesiosis was significantly higher in summer season (OR=9.0, P=0.004) followed by rainy (OR=7.43, P=0.008) compared to winter season. The risk for anaplasmosis in buffaloes increased by 3.46 times (OR=3.64, p=0.027) in non descriptive breed compared to well defined breed.