Rutaceae have attracted considerable attention because of the wide chromosome-number variation. Cytoevolution of the genus Boronia, with n=7-36, has been controversial. The critical issue is whether the base chromosome number is x=18 or x=9 in this genus and in the family Rutaceae. Phylogenetic analysis based on random amplified polymorphic DNA ( RAPD) markers was used to evaluate the hypothesis. Twenty decamer arbitrary primerswere used to produce RAPD markers in 25 accessions of 18 Boronia species and a total of 559DNA fragments was generated. UPGMA distance analysis and Wagner parsimony analysis on the DNA data produced two phylogenetic trees with very similar topology. The two trees generally supported the present classification of Boronia species. The exception was B. tenuis, which may be better treated as a new section or genus. Chromosome numbers of all the genotypes used in the analysis were counted with n=7, 8, 9, 11, 16-36. Evolutionary distances between species were determined on the basis of branch length of the Wagner cladogram. Regression analysis indicated that Boronia chromosome number has a significant negative relationship with evolutionary distance. Chromosome number in Boronia evolved from higher to lower. The basic chromosome number for Boronia is suggested to be 18.