Abstract: Marker assistant breeding, molecular breeding and genome wide breeding can shorten the generation interval of germplasm improvement and creation, speed up the selection response. Contrast with traditional best linear unbiased prediction (BLUP), they can achieve the higher genetic gain with the higher cost. Practically, together with BLUP, preselection of candidate individuals, low density array, they will become an optional choice under the consideration of selection cost and efficiency. So, in the present article, we focus on the effect of limited markers enrichment on the candidate population growth performance.e.g. body weight. For the body weight phenotype can not only be determined by one genotype, but also by multiple loci additive effect, dominant effect and epitasis. Thus, multiple loci explored needed to do variance components analysis and identify the specific genetic effect of these loci. A total of 450 fish (parents and their offspring) were collected, which were from Nanquan farm in Freshwater Fisheries Research Center in Chinese Fishery Academy. A total of 5 microstallites primers and 4 primers used for functional gene regional amplification were selected to observe the corresponded genotypes of such individuals. Correlation analysis between effective molecular markers and body weight of Huanghe carp new strain and genetic effect analysis of such markers were examined too in the present paper. The result showed that, microstallite Koi42 and 4 SNPs from the functional genes have significant effect on the carp's body weight. 13 candidate parents which have over two genotypes with higher body weight were developed. These individuals have better growth performance compared to that without these perfect genotypes. Further analysis by multiple step-wise regressions was conducted in order to make sure which markers can be implicated in practical breeding together effectively. COⅠ626, D-Loop 253 and Koi42 were left by both linear regression analysis and AIC criteria, where Koi42 has the highest contribution to the body weight variation among 3 markers. It is that Koi42 genotypes is related with sex by Fisher exact test. Genetic analysis supply the information Koi42 plays its role by additive effect (P < 0.1). Among many epitasis components, significant effect between D-Loop 253 additive effect and Koi42 additive effect was found. Through variance components partition analysis, additive variance account for 11.4%, and effect of epitasis between two loci had the higher percentage (77.5%). This told us 3 mar-kers listed above contribute to the body weight mainly by epitasis. All of these results illustrated that Koi42 with its interaction partner D-Loop 253 could be used to marker assistant breeding or multiple markers based coselection.