Area exclosures are used to minimise degradation of plant populations which are threatened by overexploitation. This study assessed the influence of a national botanical garden (area exclosure) on plant diversity and population structure. This was done by sampling in area exclosure and adjacent communal areas. Data were collected from a total of 60 (10 m × 10 m) randomly selected plots. Diameter at breast height (DBH) was measured and percentage canopy cover was estimated for all plant species. Species diversity and evenness were calculated for each site. Plant communities were classified using cluster analysis. Student t-test was used to compare diversity and evenness between the sites. Plant species composition was compared using multi-response permutation procedures. Species richness was higher in area exclosure (21) than in communal areas (12). Species diversity was significantly (p < 0.05) higher in area exclosure than in communal area. The total density was higher in area exclosure than in the communal area. The overall structure in area exclosure was healthy while the communal area showed unhealthy pattern. There were three distinct (p < 0.05) woody plant communities being Vachellia tortilis–Grewia flavescens (communal), Senegalia erubescens–Rhigozum brevispinosum (exclosure), and Dichrostachys cinerea–Combretum hereroense (exclosure). Area exclosures should be increased in Botswana to conserve woody plants.