Australia’s National Honey Bee Genetic Improvement Program, Plan Bee, was the nation’s first breeding program to implement modern breeding tools and gain the financial support of pollination-dependent industries. Plan Bee developed a nationally representative reference population, standardised trait definitions, selection criteria relevant to Australia, pedigree and performance recording spreadsheets, a national database to house beekeepers’ data and facilitate analyses, and reports to beekeepers on genotypic and phenotypic analyses which resulted in the first Estimated Breeding Values (EBVs) for Australian bees. EBVs unlock the potential for modern animal breeding, however, require sufficient quality and volume of standardised pedigree, performance and environmental data for their estimation. The Plan Bee Breeding Manual: Second edition has been developed to help queen bee breeders implement modern breeding in their enterprises and improve the genetics of Australia’s honey bee population, giving them the tools required to access EBVs for their queens. The manual outlines modern breeding principles, performance data recording using a standardised national approach and submitting that data to the Plan Bee database and contains easy-to-use, downloadable recording sheets and checklists. A trait dictionary is included, which removes ambiguity and reduces or eliminates subjectivity when recording data, and additionally covers Varroa tolerance and resistance traits.