Introduction: Scabies is known as an emerging or re-emerging parasitic disease with the prevalence are very high both in human and animals in the world. This study aims to observe the molecularly characteristic of Sarcoptes scabiei, leukocyte profile, and histopathology of rabbits’ scabies from Pasuruan and Sidoarjo, East Java, Indonesia. Methods: Twelve local rabbits from Pasuruan and Sidoarjo were used as experimental animals infected with S. scabiei, aged around 1 year old with specific clinical signs of scabies, and were clustered based on mild, moderate, and severe illness. A blood sample was collected from the auricular vein to measure the number of leukocyte and differential account (eosinophile, neutrophile, and lymphocytes). Skin histology was observed microscopically with Hematoxilyne and Eosin (HE) staining. Around 500 mites S. scabiei was isolated to detect the COX1 gene from the mitochondria of S. scabiei by PCR with primer TCTTAGGGGCTGGATTTAGTATG-3’ and 5’-AGTTCCTCTACCAGTTCCAC-3’. Results: Histopathological changes of rabbits’ skin showed parakeratosis, acanthosis, and change in the dermis with inflammatory cell infiltration, degeneration, and congestion. The PCR product with agarose gel 2% showed that the COX-1 gene in mitochondria of S. scabiei isolated from Sidoarjo and Pasuruan has length around 290 bp, and identity > 98% with gen bank data. Conclusion: S. scabiei was able to increase the leukocyte profile, and it caused histopathology changes. The molecular characterization of the COX-1 gene of mitochondria of S. scabiei of rabbits has a length of around 290 bp.