Edible bird nests (EBNs) are highly demanded globally. The industry was recently affected by an import ban to China due to high nitrite levels.Subsequently, many concerns have been raised. In this study, the microbial composition of both raw and commercial EBNs was investigated. The raw EBNs were purchased from swiftlet farms: Kuala Sanglang (Perlis), Pantai Remis (Perak), Kluang (Johor), Kajang (Selangor) and Kota Bharu (Kelantan). The commercial nests were purchased from five different Chinese traditional medicinal shops (Companies A-E) in Malaysia and one from Indonesia (Medan). A total of 123 and 34 isolates were successfully identified from unboiled raw and commercial EBNs respectively. The highest average CFU (1.77 x 104) was associated with raw EBNs obtained from Kluang, while for the commercial EBNs, those obtained from Company M1 had the highest CFU (5.50 x 104). Bacillus sp. accounted for the highest isolated species from both unboiled raw and commercial EBNs. Bacillus sp. and Brevibacillus sp. were mainly isolated from the boiled EBNs. Bacillus spp. were the dominant bacterial groups in all the raw EBNs except for those obtained from Kajang. The average number of bacteria isolated from the raw EBNs (average = 7) was higher compared with those isolated from the commercial EBNs (average = 4). The highest average number of bacterial isolates was reported in the raw EBNs obtained from Kota Bharu. Among the commercial EBNs, one EBN sample each from Companies A and M1 showed the highest number of isolates (n = 10). In general, there was a significant reduction in the number of bacteria isolated after boiling the EBNs. Raw EBNs obtained from Kajang had a distinct pool of bacterial species where the majority of the isolated species belonged to Staphylococcus species. The associated health impacts of these microorganisms to the consumers and public need to be addressed.