We compared seedling emergence and soil seed bank composition under an Acacia mangium plantation and an adjacent tropical heath forest in the Andulau Forest Reserve, Brunei Darussalam. Soil samples were collected from ten 20 x 20 m plots set up in three contrasting habitats: the Acacia plantation, the adjacent heath forest, and the transition zone in-between. Soil samples were subjected to smoke and heat treatments, following which seedling emergence was observed daily over a 12-week period. In a parallel investigation, variations in species richness, seed density and seed viability of the soil seed banks of the ten plots were investigated. Seedling emergence was significantly highest in the plantation and lowest in the heath forest plots respectively. However, no significant differences among treatments, and no significant treatment-habitat interactions were detected. Species richness, seed density and seed viability in the plantation plots were significantly lower than the transition zone and intact heath forest plots. A. mangium seeds were not recorded in the heath forest soil seed banks but were detected in the plantation and transition zone plots. Lower native plant species richness, seed density and viability in the A. mangium plantation could imply higher regeneration potential for the heath forest habitat if severe habitat destruction was to occur in this forest reserve. We suggest that proper plantation management practices and close monitoring of soil seed banks are the best mechanisms that could be adopted to minimize the gradual spread of invasive Acacias into natural tropical heath forests of Borneo.