Occurrence and importance of spoilage related bacteria in fresh Pacific white shrimp (Litopenaeus vannamei) under modified atmosphere were demonstrated in the current study. Culture-independent method including PCR-DGGE (V3 region of 16S rRNA gene), displayed a fingerprint of microbial DNA extracted directly from shrimp. Four batches of raw shrimps packaged under 80% CO₂/5% O₂/15% N₂, 80% CO₂/10% O₂/15% N₂, 80% CO₂/20% O₂, as well as unsealed packages for shrimp used as the control were stored at 4 °C during 10 days of storage. Results showed that the initial dominant bacteria of shrimp were Vibrio albensis, Vibrio sp., Photobacterium damselae, Shewanella putrefaciens, Vibrio harveyi and Vibrio parahaemolyticus. After 10 days of storage, Vibrio sp., Shewanella sp., Photobacterium damselae, Listonella anguillarum, Shewanella baltica, Uncultured Aeromonas sp. and Aeromonas veronii dominated in shrimps packaged in air. Modified atmosphere packaging (MAP) showed an inhibitory effect on several bacterial species such as Shewanella sp., Listonella anguillarum, Uncultured Aeromonas sp. and Aeromonas veronii. In conclusion, this study showed the benefits of the use of culture-independent method to enhance understanding of the composition of microbial flora in shrimps under different MAP conditions.