The invention discloses a microsatellite deoxyribonucleic acid (DNA) molecular marker of lycoris. 33 microsatellite DNA-containing clones are obtained and 10 microsatellite molecular markers with rich polymorphism, namely Lyra-1, Lyra-2, Lyra-3, Lyra-4, Lyra-5, Lyra-6, Lyra-7, Lyra-8, Lyra-9 and Lyra-10, are determined by establishing a lycoris microsatellite (CT)n enrichment library, screening and sequencing the positive clones of the microsatellite. The marker can be used for researching genetic diversity protection of the lycoris and variation and evolution relation between species and populations of lycoris plants and identifying the varieties of the lycoris; and the marker has high repeatability and is a reliable and effective molecular marker.