Comfrey Symphytum officinale L. (true comfrey) and S. × uplandicum Nyman (a hybrid between S. asperum Lepech × S. officinale L., Russian comfrey) are used externally for the treatment of pain, inflammation and swelling of muscles and joints in degenerative arthritis, in acute myalgia, sprains, contusions and strains after accidents. Besides plant secondary compounds associated with beneficial activities (e.g. rosmarinic acid and allantoin) comfrey forms also toxic pyrrolizidine alkaloids (PA). To improve further breeding and study the genetic relationships of a comfrey collection, a sample set of 219 S. officinale and 5 hybrid plants of S. × uplandicum were analysed with 34 SNP markers by KASP (Kompetitive Allele Specific PCR), developed from a next generation sequencing approach of three different individuals of S. officinale. In parallel, the plants were analysed for the polyphenol rosmarinic acid, the purine derivative allantoin, and the toxic pyrrolizidine alkaloids. Besides the two beneficial compounds, further 13 polyphenols and 10 purine derivatives were determined. The plants were grouped into six distinct genetic clusters. Rosmarinic acid was not linked to any of the clusters, while one cluster was distinctively different for some compounds, amongst them allantoin and globoidnan A. Also linked to a certain genetic cluster was a low content of PA, which could become a valuable gene pool for minimizing PA content by breeding. A subset of the samples was analysed in a second year again where rosmarinic acid and allantoin showed a medium stability, while globoidnan A was completely unstable.