Kaya Muhaka Forest in the Kenyan Coast is one of the remaining lowland forest patches belonging to Zanzibar-Inhambane vegetation mosaic of Eastern Africa, which are rich in endemic and threatened flora and fauna. Although gazetted and protected as a national monument, the forest biodiversity is still endangered. This research attempted to establish the Diversity of flora along disturbance gradient ranging from the forest core to the agro-ecosystems of the forest. The belt transect method was used where quadrats of 20m x 20m placed at intervals of every 250 m were systematically selected along two parallel transects of 3 km long each and all the plant species recorded. An additional nine plots of similar size and placement were surveyed on three parallel transects of 1km each established from the edge of the forest to the forest core. The flora diversity was calculated by use of the Shannon-Wiener Diversity Index.There was a high diversity of plant species in the Kaya Muhaka forest and agro-ecosystems. The forest was found to be homogenous with most of the species being indigenous and endemic. The forest edge was the most diverse while the forest core was the least diverse with the species richness steadily increasing from the forest core towards the edge. There was no significant difference in the species diversity between the forest core, forest edge and agroecosystems. The forest edge contained a higher Shannon-wiener diversity index of 5.25 as compared to the forest core which had a Shannon-Wiener diversity index of 4.70. The general trend showed that the diversity reduced from the forest edge to the forest core. A total of 493 species were recorded from 97 families with Papilionaceae (7.9%), Rubiaceae (6.8%), Euphorbiaceae (5.4%), Moraceae and Caesalpiniaceae (4.1%) being the most represented. The high floral diversity displayed is probably a result of frequent disturbances from the surrounding resource poor farmers.