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Biodiversity conservation is one of the important ecosystem services that has been negatively impacted by anthropogenic activities. Natural forests (NF) harbor some of the highest species diversity around the world. However, deforestation and degradation have resulted in reduced forest land cover and loss of diversity. Homegarden agroforestry (AF) systems have been proven to be an intermediary for biodiversity conservation. In this study, we evaluate the effectiveness of home garden AF practices to conserve tree species diversity in Bangladesh and compare them with tree species diversity in NF. A total of nine locations were selected for this synthesis from published literature which comprised of five AF sites and four NFs. Shannon–Weiner Diversity Index (H) was similar for home-garden AF (3.50) and NF (2.99), with no statistical difference between them. Based on non-metric multi-dimensional scaling (NMDS) ordination analysis, the AF and NF plots showed distinct separation. However, Bray–Curtis dissimilarity index ranged from 0.95 to 0.70 indicating nearly no overlap in species composition to significant overlap between AF and NF. Based on our results, we conclude that AF can serve as an important ecological tool in conserving tree species diversity, particularly on landscapes where NF fragments represent only a small fraction of the total land area. Creating and maintaining AF habitats in such human dominated landscapes should be part of the biodiversity conservation strategy.