This study was performed to investigate the species relationships and variation of Lycoris Herb. (Amaryllidaceae) species using random amplification of polymorphic DNA (RAPD) markers. Also, single nucleotide polymorphisms (SNPs) of internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2 regions in Lycoris sanguinea var. koreana were analyzed. All accessions formed 6 major clusters; cluster A with all L. sanguinea and L. chejuensis; cluster B with 3 accessions of L. flavescens; cluster C with 8 accessions of F. flavescens var. flavescens; cluster D with 10 accessions of L. uydoensis; cluster E with L. chinensis var. sinuolata and 4 accessions of L. uydoensis; and cluster F with all L. radiata. Five haplotypes were observed; L. sanguinea and L. chejuensis having the haplotype 1 with bases of CTTATATATAT; L. chinensis var. sinuolata and all L. flavescens. Lycoris incarnata and L. aurea, non-endemic to Korea had haplotype 2 and 5, respectively. Genetic variations in L. flavescens, L. chinensis var. sinuolata, and L. uydoensis are revealed based on the analysis of molecular variances (AMOVA) and haploid types analyzed by sequence analysis. It is suggested that L. chejuensis may result from hybridization involving L. sanguinea var. koreana due to a close affinity between L. sanguinea complex and L. chejuensis. Nomenclature for L. chejuensis and L. flavescens whether they should be described as a hybrid origin should be discussed in the future.