In this article, 106 microsatellite markers were used to analyze the genotype of sixty-two mitotic gynogenetic doubled haploids of Japanese flounder, Paralichthys olivaceus. Measurement results of body length and height were got by directly measuring skeleton during the process of X-ray imaging. Correlation and regression analysis of the body weight, length and height were conducted by utilizing SPSS 13.0 software. Least square method was used to analyze the effects of these 106 microsatellites on body weight, length and height of these 62 doubled haploids. Results revealed that 17 microsatellites were discovered to be very significantly related to body weight, length and height. During these 17 markers, Poli2042TUF, Poli1980TUF, Poli2045TUF, Poli2039TUF, Poli34TUF, PoGT17, HLJYP45, HLJYP81 had a significant impact on body length (P<0.05), Poli102TUF, Poli136TUF, Poli62MHFS, 6-G3 had a significant impact on body height (P<0.05), Poli72HFSM、Poli106TUF had a significant impact on body weight and height (P<0.05), Poli2023TUF, Poli1013TUF had a significant impact on body length and height (P<0.05), Poli162TUF had a significant impact on body weight, length and height (P<0.05). These microsatellite markers had an advantageous effect on growth traits and these loci could be used as the reference markers for marker-assisted breeding of Japanese flounder.