Abstract:A new species of Sophora(Leguminosae), S. elongata S. P. Chen & W. J. Lin, was found in Wuyishan National Park, Fujian Province, which was most similar to S. flavescens in morphology. Their difference between the two species was that the plant was short, the raceme was 40 cm, and the calyx was 2 mm×3 mm. The phylogenetic tree constructed based on three nuclear DNA fragment combinations (ETS, ITS, SQD1) and four chloroplast DNA fragment combinations (matK, rbcL, rpl32-trnL, trnL-F) showed that S. elongata had an independent position on the phylogenetic tree, which supported that S. elongata was a new species of Leguminosae, but its phylogenetic position was independent and there was nuclear-cytoplasmic conflict, presumably due to ancient hybridization or incomplete phylogenetic sorting.