ABSTRACTA big F1 population of ‘FengliduoxDawuyuan’ were created by crossing between a high quality cultivar ‘Fengliduo’ and a large fruit size main cultivar ‘Dawuyuan’. Among the Hybrid population, 94 F1 individuals were randomly chosen and used as the mapping population. Based on the mapping population, a molecular genetic linkage map of longan was constructed with RAPD, ISSR, SRAP and AFLP molecular markers. According to the linkage analysis by JoinMap3.0, the molecular linkage map of ‘Fengliduo’ fell into 20 linkage groups, which contained 184 markers, with an average interval of 6.72 cM and covered a total distance of 1102.8 cM; while the molecular linkage map of ‘Dawuyuan’ fell into 19 linkage groups, which contained 243 markers, with an average interval of 6.02 cM and covered a total distance of 1348.3 cM. The IM method was used to determine QTL associated with some traits in this population. 29 QTLs related to fruit weight, soluble solid content, seed weight, peel weight and edible rate were identified in 20 linkage groups of parents.