Nosema disease in honey bees (Apis mellifera) is caused by either the microsporidium, Nosema apis or Nosema ceranae. It has been proposed that N. ceranae originated in east Asia as a pathogen of Apis cerana, and then spread worldwide infecting A. mellifera. To examine this, the genetic variation of N. ceranae samples from Vietnam, Iran, Ontario-Canada, Alberta-Canada, United States, Mexico and Argentina was investigated using novel genetic markers for this pathogen, simple sequence repeat (SSR) length polymorphisms and translation elongation factor-1 alpha sequence. Both markers showed that the highest genetic variation was in Vietnam, and the translation elongation factor-1 alpha sequence showed that only the most common genotype in Vietnam was detectable in other parts of the world. The SSR length polymorphisms also detected some variation in other parts of the world, which corresponded to the international movement of honey bee queens. The results are consistent with N. ceranae being an invasive species with a subset of N. ceranae genotypes spreading from southeast Asia. Several microbial-derived products were tested for their ability to induce innate immunity against nosema disease in A. mellifera. Feeding chitosan or peptidoglycan significantly reduced spore numbers and altered expression of the antimicrobial peptide genes, hymenoptaecin and defensin2, and the autophagy-related gene, blue cheese, of adult honey bees. A study on the effect of N. ceranae infection, as well as infection along with chitosan and peptidoglycan treatment revealed that hygienic behaviour of A. mellifera was not affected by infection or treatment. However, chitosan or peptidoglycan treatment stimulated foraging behaviour. Peptidoglycan and N. ceranae infection without treatment did not alter the proboscis extension reflex (PER), but chitosan significantly decreased memory retention on the first day, but not later days, of the PER test. Chitosan and peptidoglycan treatment also increased the survivorship compared to N. ceranae infection without treatment. Chitosan and peptidoglycan are promising alternative treatments for nosema disease, reducing pathogen reproduction, increasing longevity and stimulating foraging behaviour.