Current long read sequencing, e. g. PacBio and Nanopore, requires high molecular weight (HMW) and highly pure DNA. Many fungal and plant species have high content of polysaccharides and other contaminants that are co-precipitated with DNA during ethanol precipitation. This protocol aims to purify HMW DNA from the DNA solution obtained using Benjamin Schwessinger's protocol (dx.doi.org/10.17504/protocols.io.ewtbfen).The protocol was tested fuccessfully in wheat leaf rust, barley leaf rust, wheat stem rust and myrtle rust.Critcal step to seperate HMW DNA from low molecular weight DNA and other contaminants during ethanol precipitation is to allow cotton-fiber-like HMW DNA to sediment by gravity, while other small molecule DNA and contaminants remain in the supernatant.