This study investigated the identity, growth and metabolite production of micro-organisms causing spoilage of Pangasius hypophthalmus fillets packaged in air, vacuum and modified atmospheres (MAP) (MAP 1: 50%CO(2)-50%N(2) and MAP 2: 50%CO(2)-50%O(2)) during storage at 4 °C. Based on the time it took for psychrotrophic total colony counts to exceed 7 log cfu g(-1), the shelf life of the fillets packaged in air, vacuum, MAP 1 and MAP 2 was estimated to be 7, 10, 12 and 14 days respectively. The longest lag phases were observed in the samples packaged in MAP 2 (50%CO(2)-50%O(2)). In the fillets packaged in air and under vacuum, the dominant flora identified by partial 16S rDNA sequencing at the end of the shelf life generally consisted of Gram-negative bacteria mostly belonging to the genera Serratia and Pseudomonas. In contrast, lactic acid bacteria (Carnobacterium maltaromaticum and Carnobacterium divergens) and Brochothrix thermosphacta were identified as the dominant spoilage flora in the samples packaged under the two MAPs investigated. By means of solid-phase microextraction gas chromatography mass spectrometry (SPME GC-MS) analysis, volatile organic compounds in the headspace of the samples at the end of the shelf life were identified for each packaging condition. Based on these results, a selective ion flow tube mass spectrometry (SIFT-MS) method was developed to quantify the production of volatile metabolites during storage of the fillets. The results of these analyses indicated that several compounds contributed to the bacterial spoilage of Pangasius fillets e.g., ethanol, 2,3-butanediol, diacetyl, acetoin, ethyl acetate, acetic acid and sulfur compounds. It also emerged that the production of these compounds was dependent on the packaging condition applied.