The isolation of nuclear genomic DNA of high molecular weight is becoming a crucial step for obtaining long read sequencing data produced by the PacBio and Oxford Nanopore platforms. Although it involves a few more steps than a standard total genomic DNA preparations, it is worth optimizing the protocol to avoid wasting valuable sequence data on organellar DNA. The current protocol has been successfully applied to kiwifruit, apple, mānuka, Nicotiana benthamiana, some solanaceas, and two insects (pupae of the light brown apple moth (Epiphyas postvittana) and hind leg of a weta (Deinacrida spp)). Three alternative methods to extract DNA are also presented.