The genus Boronia Sin. section Boronia series Boronia contains species with n = 7 (B. megastigma), n = 7 or 8 (B. heterophylla), n = 8 (B. molloyae) and n = 9 (B. purdieana), representing ideal species with which to examine comparative chromosome morphology. Between species there were few chromosomes with similar morphology, indicating numerous genome re-organisations. Karyotypes between and within species of Boronia could be distinguished and inheritance of some chromosomes was observed. Species and hybrids with 2n = 14 or 15 had at least one large chromosome. Chromosome morphology indicated a closer relationship between B. heterophylla and B. molloyae and between B. purdieana and B. megastigma than between these two groups. Whole genomic DNA was extracted from 9 genotypes of Boronia. RAPD bands were analysed and pairwise distance matrices between genotypes were computed. Dendrograms were generated and analysed using unweighted pair-group method with arithmetic average Cluster analysis. Dendograms supported cytological results, indicating B. heterophylla and B. molloyae are closely related ad clearly distinct from B. megastigma and B. purdieana. The evolution of boronias is discussed.