Abstract: In this study, comparative genomics of Fagopyrum chloroplasts was studied using bioinformatics methods. The results showed that the chloroplast genome sizes of the five species of Fagopyrum ranged from 159 265 to 159 599 bp; the GC content ranged from 37.81% to 37.98%, and there was a small difference in the number, type, and copy number of genes; The regional boundaries were basically consistent; The type and number of SSR types were similar; The polymorphism of LSC and SSC in this genus was higher than that in IR region, and the non-coding regions trnS-trnG, rps4-TrnT and rpl32-TrnL were the hot-spot region with the highest variation; Systematic analysis showed that F. leptopodum had the closest genetic relationship with F. tataricum.