Background: The study was aimed at molecular detection and assessment of important biomarkers in the natural cases of canine babesiosis. Methods: Blood samples of 239 dogs were examined in PCR by targeting 18S rRNA gene. Hematobiochemical, oxidant-antioxidant and plasma cortisol parameters were estimated in the dogs on the day of presentation. Result: The 18S rRNA gene sequence showed 100% homology with Babesia canis vogeli and phylogram formed a tight cluster of B. canis vogeli originated from India/other countries. Higher prevalence rate (P<0.05) was noted in the PCR (7.95%) than the cytological technique (3.76%). Hemogram of infected dogs showed decrease (P<0.05) in the mean value of hemoglobin, RBC, WBC, HCT, whereas an increase in MCHC, lymphocytes, eosinophils, monocytes and thrombocytes. The ALT (49.29 +/- 1.53 U/L), AST (48.33 +/- 2.93 U/L), total protein (10.56 +/- 0.60 g/dL), creatinine (1.41 +/- 0.10 mg/dL) and urea (19.32 +/- 0.97 mg/dL) showed significant (P<0.005) increase, whereas decrease in the levels of serum glucose (82.76 +/- 2.78 mg/dL) in the infected dogs. Activity of MDA and SOD was significantly (P<0.01) increased (7.50 +/- 7.08 nmole/mu L blood) and decreased (0.015 +/- 3.91 nmole/mu L blood) in the diseased dogs, respectively. Plasma cortisol concentration was 11.10 +/- 7.84 nmol/L and 2.77 +/- 5.78 nmol/L (P<0.01) in the infected and uninfected dogs, respectively.