Abstract: A genetic linkage map for loquat was established based on 56F1 population derived from the cross between Zao Zhong No.6and Gui Fei loquats using JoinMap 4.0software.The map consisted of 19 linkage groups including94 genetic markers (i.e., 23 SSR markers, 28 ISSR markers, 42 SRAP markers and 1flesh color GRYS trait) .The map covered 849.0cM of the genome.The average length of the genetic linkage group was 44.7cM, and the average distance between the adjacent loci was 9.1cM.Each group contained 2to 16 loci, and 4.9 markers per group.The marker linked to the flesh color of the fruits was located in between S33-250 and UCB842-1 000 in Group 5.