There are few published studies on various vector borne diseases of dogs in India and most depict clinical infection in dogs, diagnosed by observation of the haemopathogens in stained blood smears. This study provides the first report regarding molecular confirmation and ancestral relationship analysis of blood smears positive cases of assorted haemopathogens in Punjab province of India. On blood smear examination, haemopathogens were observed in 124 out of 778 (15.95%, 95% CI: 13.53– 18.68) blood smears. Further polymerase chain reactions (PCR) was used on bloods smear positive cases to validate the results. Out of 778 blood samples, Babesia gibsoni was most common parasite infecting dogs (15.04%, 95% CI: 12.7–17.72), followed by Ehrlichia canis (0.39%, 95% CI: 0.0–1.13), infection of Babesia vogeli and Hepatozoon canis was same (0.26%, 95% CI: 0.0–0.9). Among various risk factors studied (age, sex, season), prevalence of infection was non-significantly higher in 1–2 year of age group (19.88%, 95% CI: 14.45–26.71), regarding sex same prevalence was recorded (15.94%), and chances of infection was highest in pre-monsoon i.e. summer (18.26%, 95% CI: 14.49–22.76). Phylogenetic analysis revealed ancestral background of Ludhiana isolates of B. vogeli , B. gibsoni, H. canis , and E. canis with the isolates of Philippines, Mongolia and Tunisia.