The beauty of conserving germplasm is the securement of genetic resources with numerous important traits, which could be utilized whenever they need to be incorporated into current cultivars. However, it would not be as useful as expected if proper information was not given to breeders and researchers. In this study, we demonstrated that there is a large variation, both among and within germplasm, using a low-cost image-based phenotyping method; this could be valuable for improving gene bank screening systems and for crop breeding. Using the image analyses of 507 accessions of buckwheat, we identified a wide range of variations per trait between germplasm accessions and within an accession. Since this implies a similarity with other important agronomic traits, we suggest that the variance of the presented traits should be checked and provided for better germplasm enhancement.