show Abstracthide AbstractCannabis has been carried around the earth by humans for 1000s of years and used as medicine, food, fiber, and fuel. However, we understand very little about genetic variation in modern cultivars and how we can improve the plant for its many uses. Most modern genomic and molecular breeding tools, such as a high quality, annotated genome sequence and methods for creating doubled haploids are unavailable. In recent decades, breeding has been unstructured and with limited knowledge of genetic variation in parental lines, which has led to a diversity cultivars. We have characterized the genetic variation in modern Cannabis as well as putative landraces in an effort to develop markers and tools for breeders. We developed a web-based application for 3D visualization of Cannabis population structure that can be used to choose cultivars for breeding or research.