Pugu Forest Reserve is part of the Coastal Forests of Eastern Africa Hotspot, recognized as one among the 34 global biodiversity hotspots. Fire unselectively devastated many favorable habitats and directly killed a substantial number of plant species in 2008 in the northern part of the Pugu Forest Reserve. The aim of the study was to assess natural regeneration of indigenous plant species five years after that fire. Sampling was performed using a nested plot design along three transects established among the topographic positions of hill tops, hill slopes and valley bottom. It documented 116 indigenous plant species from 46 families that had successfully regenerated in the burnt area. The stem densities of woody plant species differed significantly among the three topographic positions. The results of this study indicate higher densities of coppiced trees, sprouts, and seedlings on ridge tops versus hill slopes and valley bottoms. The species Garcinia acutifolia, Fernandoa magnifica, Rothmannia macrosiphon, Baphia puguensis and Uvaria decidua were among the threatened plant species under the International Union for Conservation of Nature (IUCN) Red List that failed to regenerate in the ridge tops. The impacts of the fire modified the natural habitat characteristics of the forest, causing some plant species to shift their normal distribution ranges. This study concludes that the forest recovery observed following the 2008 fire highlights the importance of fire suppression in effective conservation management strategies of the Pugu Forest Reserve.