Isolating and analysing an organism’s DNA is key for developing insights into species or strain identification, for uncovering variants useful in breeding or a more thorough understanding of biology, and for discovering the microbes carried by individuals. DNA extraction methods must be robust for small amounts of starting material even if that material has become degraded. They must deliver extracted DNA of sufficient quality, purity, and quantity for downstream efforts ranging from target identification (e.g., via the Polymerase Chain Reaction, PCR, below in), sequence analysis, and cloning, among others. Below are tested protocols for common DNA analyses of diverse bee samples, starting with the isolation and purification of DNA. Isolating DNA from tissues can be accomplished using a variety of commercial kits, or via procedures built on standard disrupting and separating agents as below. Here we describe protocols made from primary ingredients, since this is illustrative of the critical components in these and pre-made extraction protocols.