Bacillus cereus, responsible for food poisoning and Clostridium difficile, causative agent of Clostridium difficile-associated diarrhoea (CDAD) are both spore forming pathogens. Spores are important players in food spoilage, food intoxication and other infections in humans and animals. The proteinaceous coat and exosporium layers from spores are important for their resistance and pathogenicity characteristics. The exosporium additionally provides an ability to adhere to surfaces eventually leading to spore survival and spoilage in food. Thus studying these layers and identifying suitable protein targets for rapid detection and removal of spores is of utmost importance. In this study, we identified 100 proteins from B. cereus spore coat, exosporium and 54 proteins from the C. difficile coat insoluble protein fraction. In an attempt to define a universal set of spore outer layer proteins we identified 11 superfamily domains common to the identified proteins from two Bacilli and a Clostridium species. The evaluated orthologue relationships of identified proteins across different spore formers resulted in a set of 13 coat proteins conserved across the spore formers and 12 exosporium proteins conserved in the B. cereus group which could be tested for quick and easy detection or targeted in strategies aimed at removal of spores from surfaces.