Clones serve as an important function in immunological, endocrinological, developmental biological, molecular biological and genetic studies; however, poor fertility of doubled haploids effectively hinders the production of homozygous clones, with the result that only a few laboratories have succeeded in producing homozygous clones. Protocol studies and studies into the biological characteristics of clonal fish are well known and ongoing but, to the best of our knowledge, there have been no hematology studies. This research study is a comparative analysis of the hematology of clonal and common Japanese flounder using 10 physiological parameters and 17 biochemical indices. At Beidaihe Central Experiment Station, clonal flounder were produced by gynogenesis that suppressed cleavage of the eggs in mitosis and then blocked the extrusion of the second polar body in meiosis. The results showed that red blood cells (RBC), hemoglobin (HGB), mean corpuscular hemoglobin (MCH) and hematocrit (HCT) of clonal Japanese flounder were significantly lower than that of common Japanese flounder (indices between clonal and common Japanese flounder. In addition, blood biochemical indices – alkaline phosphatase (ALP), cholesterol (CHO) and blood urea nitrogen (BUN) – for clonal Japanese flounder were significantly lower than for common Japanese flounder (<0.01). However, albumin/globulin (ALB/GLB), aspartate aminotransferase/ (AST) were significantly higher for clonal Japanese flounder than for common Japanese flounder. The average coefficient of variation (CV) for the physiological was 5.50% for and 9.21% for common Japanese flounder. The mean corpuscular volume (MCV) coefficient of variation for clonal was only 1.52%. The average blood biochemical indices between clonal and common Japanese flounder were 10.56% and 27.23%, respectively.