A new species, Fritillaria yakutiae (Liliaceae), is described from the Babatag Range in the Surkhandarya region of Uzbekistan. The species is placed within the subgenus Rhinopetalum of the genus Fritillaria. Morphologically, F. yakutiae closely resembles F. bucharica and F. baisunensis but differs in key floral characteristics, including the color and pattern of the perianth and anthers. Phylogenetic analyses based on complete chloroplast genome sequences confirm its placement within the Rhinopetalum clade, forming a strongly supported sister relationship with F. bucharica, F. gibbosa, and F. baisunensis. The chloroplast genome of F. yakutiae has a total length of 151,757 bp and contains 130 annotated genes, including 84 protein-coding genes. The species is currently known only from its type locality, where approximately 300 mature individuals were recorded in 2020. Given the limited available data on its distribution and population trends, F. yakutiae is assessed as Data Deficient (DD) under the IUCN Red List criteria.