Microbiomes can either help or resist pathogens, but so far little is known about swine tonsil microbiomes – a location with many pathogens. Samples were taken from healthy and unfit swine tonsils and compared. Unfit pigs had a greater diversity of bacteria, and associations were found between the presence of Mycoplasma and illnesses including anemia, abscesses, and PRRS. Both healthy and ill animals had Streptococcus sp., Flavobacteria sp.,Clostridia sp., Lactobacillus sp., Bacillus sp., and Fusobacterium sp. Unfit animals were  more likely to have Actinobacteria and Fusobacteria, and healthy animals had more Firmicutes, Spirochaetes, and Streptococcus sp.