The genus Dodonaea (Sapindaceae) comprises slightly over 70 species. Dodonaea viscosa is a plant of Australian origin with seven subspecies. In Kenya, there are two subspecies. D. viscosa has been used medicinally to manage several ailments. It is considered a difficult taxonomic group due to its polymorphic nature. Owing to its uses in ethnomedicine and the taxonomic challenge of Kenyan subspecies, a molecular phylogenetic study was done using ITS1 and rbcL genes from Kenyan populations. DNA was extracted, sequenced, exported to MEGA 11, PhyloSuite, and R for analysis. Aligned sequences were subjected to evolutionary analyses and PCA while phylogeny was constructed using maximum likelihood (ML) method. Nucleotide frequency and substitution rates, nucleotide disparity index, and evolutionary divergence of the genes were very low implying a short genetic distance among the Kenyan populations. ML trees showed that the highland and coastal Dodonaea populations were closely related as they are monophyletic and have high bootstrap values. PCA showed that rbcL genes contributed to most variations in Dodonaea populations where two clusters based on rbcL genes were observed. In contrast, ITS1 genes contributed to fewer variations and grouped all Dodonaea populations into one cluster. This study provides more data to solve the taxonomic challenge of D. viscosa. There is a need for further studies targeting other gene regions to understand well the phylogenetic relationships of Kenyan populations of Dodonaea.