The present article describes the use of broad-range molecular analyses to characterise the microbial population of farmed Atlantic cod (Gadus morhua) packaged for the retail market. Cod was filleted post rigor, packaged in air or in modified atmosphere (MA) (50% CO(2):50% N(2) or 50% CO(2):50% O(2)) and stored at 0 degrees C for 11 days. To determine the community profiles of the samples the variable V3-region of the bacterial 16S rRNA gene were amplified by PCR, before the PCR products were separated by denaturing gradient gel electrophoresis (DGGE). From sequence analyses Pseudomonas spp. were found to be the predominant bacteria in oxygen enriched atmospheres, whereas the spoilage bacteria Photobacterium sp., Shewanella putrefaciens and Pseudomonas spp. dominated in CO(2):N(2) and air packaged samples. Additional microbial analyses by cultivation methods observed highest bacterial numbers in air stored samples, and both MA mixtures gave growth inhibition when measuring aerobic plate count, psychrotrophic bacteria and H(2)S-producing bacteria. The results show that PCR-DGGE can be applied to examine bacterial diversity and population shifts among different MA-packaged products.