Commercial fishery catches in Brunei Darussalam between 2000 and 2009 were used to examine changes in community structure of Brunei's marine ecosystem – a relatively lightly harvested system within a region chronically overexploited by fisheries. We found that Mean Trophic Level (MTL) has declined at a rate of 0.08 trophic levels (TL) per decade, suggesting a ‘fishing down the marine food web’ process in Brunei waters. In order to focus on changes in relative abundance of the more threatened, higher TL finfish only, MTL was recalculated as 3.30MTL (to exclude catches of finfish and invertebrates species with TL less than 3.30). Here, we found no overall trend in the 3.30MTL over the study period. However, a more in-depth analysis suggested that MTL fails to capture substantial changes in underlying species assemblage. Over the course of the study period, marked changes in fish community structure were observed. Analysis of official statistics showed an increase in total catch was driven primarily by an increase in pelagic catches, with a similar trend observed when the catches were aggregated into either high- or low-TL. This pattern is consistent with the increasing Fishing-in-Balance (FiB) index for the Brunei region. Whilst our study was not aimed at demonstrating overfishing as the cause of observed trends, there is a danger that current best practice fails to detect what may be an imminent fishery collapse. In many fisheries around the world, there is a need for detection methods able to identify potential problems within a time scale short enough to be able to react effectively