Results of the genetic study indicate that genetic polymorphisms can be used when comparing botanical remains to identify the variety of B. pilosa present at a crime scene to detect the genetic variation of these loci. Botanical specimens found at a crime scene might provide valuable information when determining a primary geographic location, especially for plants that rely on animal dispersal. Bidens species produce barbed fruits and are a wide-spread herb in Taiwan. Parts of the plant are considered valuable because of their photochemical properties. The flora of Taiwan sub-divides Bidens pilosa L. into three varieties, var. radiate, minor, and pilosa. Based upon 168 samples in this study, inter-species variation between B. biternata and B. pilosa were determined. Distinct types were present in B. biternata at the four loci and could be differentiated from B. pilosa. These four loci have shown the potential to differentiate the inter-specific differentiation in Bidens species. Fragments of these three varieties are difficult to differentiate by traditional morphological characteristics and until now little was known of their genetic composition. To discover genetic polymorphisms among these varieties, five loci within the nuclear and chloroplast genomes were screened. A total of 161 specimens were used in this study comprising different geographical populations. DNA fragments of all samples at the trnL intorn, and trnL-trnFIGS loci of the chloroplast genome, internal transcribed spacer (ITS1 and ITS2), and the 5.8S of nuclear ribosomal DNA were amplified and sequenced. The sequence types for any locus of trnL intron, ITS1, ITS2, and 5.82 were found to be useful markers to identify Bidens biternata and the three varieties of B. pilosa. The resulting 84 haplotypes at the 5 loci could differentiate the var. radiate from the varieties of B. pilosa with the exception of one type. Tables, references