Cannabinoids are a large section of the Cannabis market which has created new opportunities and challenges for industry and academia. Breeding Cannabis sativa L. plants to have specific chemical profiles for all aspects of the industry takes time and resources, which requires new methods to help accommodate those needs. These protocols were developed to create less resource intensive methods for testing chemotype segregation of young cannabis plants. This protocol can be used for breeding new cultivars of Cannabis and help cull plants with undesirable chemotypes at a younger age, along with testing plants in a less harmful manner for further growth. Creating two methods, one for HPLC and the other for a LightLab 3 Cannabis Analyzer, provides more options for chemotype determination for breeding and testing of Cannabis and shows the limitations of testing using these methods.