We have been investigated the microorganisms associated with bees both parasites and microflora. Objectives are (1) to analyze the viral genomes to elucidate the host-parasite relationship between virus and the honey bee (Apis mellifera) (2) survey the viruses parasitized in our Thai bees in the Northern Thailand (3) to study the lytic enzymes from the fungus causing Chalkbrood diseases in honey bee and to compare the enzymatic patterns from isolates of different geographic origins (4) to study the diversity of microflora of honey bees and stingless bees found in Northern Thailand and secondary metabolites produced by the microflora. Results were (1) by using bioinformatics tools, the co-evolution of codon usage of six bee viruses towards that of the honey bee was clarified. This suggested that small host specific viral genomes had the freedom to quickly optimize codon usage to successfully parasitize their preferred host (2) six bee viruses were surveyed and found that the most prevalent virus was deformed wing virus and the acute bee paralysis virus (3) enzymatic pattens were similar between strains of the Chalkbrood pathogen found in Thailand. Protease and Nacetylglucosaminidase from the fungal pathogen were purified and studied. (4) Actinomycetes were isolated and identified. Most were belong to genus Streptomycetes. Yeasts and bacteria were identified and described. The future application by using yeast capable of using xylose and some bee microflora producing antimicrobial activities against bee pathogen were demonstrated.