Construction of genetic linkage maps for lily was achieved using two populations, LA and AA that share one parent ÔConnecticut KingÕ. Three different molecular marker systems (AFLP TM , DArT and NBS profiling) were used in generating linkage maps for ÔConnecticut KingÕ. The LA and the AA populations consist of 20 and 21 linkage groups (LGs), respectively. Average density between markers was 3.9 cM for the LA and 5 cM for the AA population. Several horticultural traits were mapped for the first time in Lilium and showed to be single gene based. We propose to name these genes as LFCc for flower colour, lfs for flower spots, LSC for stem colour, lal for antherless phenotype and lfd for flower direction whereby upper and lower case names refer to dominant and recessive genes, respectively. Additionally, resistance to Lily mottle virus (LMoV) was mapped as a locus on LG AA10. For Fusarium resistance, the Kruskal-Wallis test identified six putative quantitative trait loci (QTL) in the AA population of which one QTL (explaining 25% of the variation in resistance) could be confirmed by interval mapping.