High density genetic map and genome sequences are important resources for molecular breeding. But for most plant species without genome sequences, lack of genome information hinders molecular breeding progress. Here we present a novel NGS-based plant molecular breeding system for such kind of crops. Lupin (Lupinus angustifolius L.) is an important grain crop domesticated in Australia after the 1960’s. The cross of Unicrop x Tanjil and the 94 F8-RILs were subjected to restriction-site associated DNA (RAD) technology with HiSeq2000 sequencing platform. Total 7079 co-dominant SNP markers identified by RAD reads were grouped into 20 linkages with ~ 1500 cM length. Using this high density genetic map, a resistance gene Lanr1 against anthracnose disease was mapped at sequence linkage group (SLG)-1, which had the closest adjacent SNP marker at 0.56 cM. Another disease resistance gene against phomopsis stem blight was mapped at SLG-4, which was flanked by two SNP markers with the genetic distances of 0.54 cM and 0.56 cM, respectively. The seed coat color gene was mapped at SLG-7, which had 18 co-segregating SNP markers. In order to figure out these genes related to traits of agronomic interest, preliminary de novo genome sequencing (30-fold data) was conducted on one parent Tanjil. These 598Mb rough genome sequences provide a great genetic resource for gene discovery with fine mapping results. By our NGS-based breeding system, many easy-used markers developed in this study linked to seed coat color gene and disease resistance genes are already applied for lupin breeding.