Some sea cucumbers species are heavily exploited as bêche-de-mer for the Asian food industry and the global decline of certain highly sought after species has generated an interest in determining the ecological function of those animals within their ecosystem. This study investigated the ecological role of Holothuria scabra, a commercially valuable tropical species closely associated with seagrass beds. Seagrass productivity, seagrass and benthic microalgae (BMA) biomass and organic matter (OM) were measured during two exclusion experiments conducted using in situ cages deployed for two months both in 2003 and 2004. Density of H. scabra was manipulated in caged exclusions (near-zero density, ‘EX’), caged controls (natural densities, ‘CC’) and uncaged controls (natural density, ‘NC’). Seagrass growth was lower when holothurians were excluded (5% in 2003, 12% in 2004). Seagrass biomass decreased in all treatments, but reduction was greater in EX than in controls (18% in 2003, 21% in 2004). Both BMA biomass and OM increased in EX compared to NC/CC (in 2004). From a multivariate perspective, a principal component biplot separated EX from both types of controls in 2004, and multivariate tests based on four attributes supported this separation. These results indicate that seagrass systems may suffer in the absence of holothurians; however, the effect size varied between the two experiments, possibly because experiments were conducted at different times of the year. Nevertheless, our results suggest that holothurian over-fishing could have a negative impact on the productivity of seagrass systems.