Biodiversity assessment for tree species was conducted in three forest fragments ofihe Taita Hills, southeastern Kenya to compare species diversity between and within three exotic forest plantations of pine, eucalyptus, cypress and the indigenous forests. The study sites were: Ngangao (120 ha), Chawia (86 ha), and Mbololo (185 ha). A Y-plot design was used to sample 32 plots comprising of 65 subplots. At each subplot, all juvenile trees of 5 cm and above in diameter at breast height (DBH) were enumerated and recorded by species. Tree regeneration (seedlings and saplings) was tallied by species. The Shannon-Weiner Index was used to calculate species diversity and evenness. The derived Shannons indices were further converted into effective numbers to show the magnitude of differences in species biodiversities. To evaluate differences in species diversities, a one way ANOVA was conducted and to separate the means, Tukeys HSD and Duncans tests were used for even and uneven number of samples respectively. Jaccards similarity index was used to assess species similarities. There were more than 58 species whose stem densities varied between 10 and 2 000 trees per hectare.There were significant differences in species diversities between forest types and sites; the indigenous forests showed higher diversities than the exotic forests. Similarly, Chawia sites had higher species diversity than both Ngangao and Mbololo. Chawia also had a higher number of regenerated species than the two other sites, including species such as Xymalos monospora, Rapanea melanophloeos, and Syzygium guineense, which are associated with low levels of disturbance. These findings indicate that the indigenous forest is more diverse in species as would be expected in the tropics. The high species diversity in Chawia could be accounted for by the higher levels of disturbance it underwent, unlike the two other sites.The regeneration of species associated with low levels of disturbance found in the exotic plots of Chawia show the likelihood of presence of long-term soil seed banks. The low regeneration in the exotics plots observed in Ngangao and Mbololo are likely due to the absence of seed banks since some of the plantations were established on bare land (in Ngango), or the inherent physiology (allelopathy) of some of species repelling the regeneration of others.