Fritillaria yakutii (Liliaceae), from the Babatag Range in Surkhandarya, Uzbekistan, is described as new. It belongs to Fritillaria subgenus Rhinopetalum, which is known for its recent diversification and morphological variation across Central Asia. Morphologically, F. yakutii 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 confirms 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. yakutii 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. yakutii is assessed as Data Deficient (DD) under the IUCN Red List criteria.