The different customer and regulatory specifications for mesophilic and thermophilic aerobic and anaerobic spore numbers in skim-milk powder, in addition to some specifications on specific spore-forming bacteria, such as Bacillus cereus, can be challenging for the industry to meet. Twenty-two samples of medium-heat skim-milk spray-dried powder from eight sources were analysed in triplicate with 16 bacterial and spore enumeration tests to understand the variety of spore-forming bacteria population. Using 16S rDNA sequencing, the species were identified for 269 isolates that were representative of the various tests. Of the isolates identified, 68% were Bacillus licheniformis, a facultative anaerobe that can survive and grow at mesophilic and thermophilic temperatures, making it difficult to eliminate in manufacturing environments. Using whole genome sequencing, 16 of 23 isolates identified as B. licheniformis by 16S sequencing were confirmed as B. licheniformis, four were identified as Bacillus paralicheniformis and three were identified as Bacillus sp. H15-1.