Abstract: This study assessed the effects of agroforestry system on diversity of native woody species and soil physico-chemical properties. This was achieved by comparing floristic composition and soil physico-chemical properties in four different Taungya agroforestry sites and a natural regrowth forest reserve where active logging has not taken place in Ondo State, Nigeria. Two sample plots of 25 m x 25 m were assessed in each site using systematic sampling techniques. All the plants were identified to species level and categorized into tree, shrub, perennial herb, scrambling shrub, epiphyte, climber and their families were identified. Shannon-Weiner and species evenness indices were used to assess and compare native woody species diversity and abundance.