Molecular markers have a wide range of applications such as marker-assisted selection,analysis of genetic diversity of germplasm resoures,constrcution of genetic linkage maps ect.RFLP,RAPD,SSR,AFLP,SCAR,CAPS,SNP are common methods of molecular markers.So far,domestic and foreign researchers have used molecular markers to marker and mapping more than 20 quality traits in watermelon and melon.Among them the RAPD molecular marker is the method that used most widely,while the advantage of SSR marker is used less than other markers.The current molecular markers major research on plant diseases and insects resistance genes,and most of the linkage markers have a lager genetic distance to the target genes,which not suitable for map-based cloing.But the basic of genetics genes have not sufficiently research.This article summarized the molecular markers and mapping of quality traits research progress in watermelon and melon.