Herbal medicine has been used for many years and it remains widespread in developing countries while the use of complementary alternative medicine is increasing rapidly in developed countries. Senna didymobotrya is important for its medicinal use among many communities to treat a wide range of ailments. The study examines the patterns of morphological variation and phenetic relationships among 39 populations of S. didymobotrya in Kenya using17 quantitative and 17 qualitative characters. A survey was carried out in Siaya, Kisumu, Nandi and Nakuru Counties to collect S. didymobotrya plants. Results on morphometric analysis indicated that the standard deviations were highly significant when all quantitative characters were considered. Stem diameter, plant height and stem height had the highest standard deviation of 13.14, 11.74 and 11.15 respectively. Leaf length and Internodal length had the lowest standard deviations of 0.18 each. Principal component analysis indicated that the plant height, stem height, stem diameter, habitat, pod length, pod width and number of seeds accounted for a cumulative percentage of 70% and above of the cumulative variance in a lineal combination of parameters hence can be used to separate the populations. Correlation matrix of the morphological characters indicated a high positive correlations between inflorescence length of basal stalk and inflorescence length (0.83), stem height and plant height (0.62), leaflet width and leaflet length (0.56), leaflet number and leaf number (0.54), pod width and pod length (0.52). The cluster analysis dendrogram placed the plants in four major clusters; Cluster 1 had one plant accession PJ/NK/33 collected from Nakuru County. Cluster II had one plant PJ/KS/13 collected from Kisumu County. In Cluster IV also had one plant accession PJ/SI/2 collected from Siaya County. Cluster III consisted of 36 plants with close relationship (Plants accessions PJ/SI/4 - 10, PJ/KS/11- 18, PJ/NA/19 - 29, PJ/NK/30 - 32 and PJ/NK/34 – 39). The highest similarities and high variations in cluster I, II, and III results that call the relationship between them in question. An identification key has been constructed which, for the first time, can be used to assign herbarium specimens to their respective taxa. Further research should be carried out to collect more samples from other regions within the country and other parts of the world to understand the morphological variations sufficiently to circumscribe the taxonomical doubts on how many species and/or lineages that do exist due to the influence of habitat type on the morphological variation between populations and if other methods like molecular markers (isozymes or microsatellites) are employed ,to reveal patterns of genetic variability. The beneficiaries of this study are the herbalists, pharmacologists, researchers, patients and the general public.