There are two cultivated and weedy types of crop (TCWTPC), and they are widely distributed and cultivated in East Asia, especially in South Korea and Japan. The objective of this study is to create simple sequence repeat (SSR) markers linked to morphological traits that show differences between accessions of the TCWTPC using recently designed SSR primer sets in crop. Genetic diversity within 52 accessions of the TCWTPC, gathered from South Korea, was assessed using 28 novel SSR primer sets. Based on the assessment, a collection of 28 SSR primer sets were shown to exhibit polymorphism and yielded a total of 142 alleles across the 52 accessions of the TCWTPC. Through inspection of a phylogenetic tree and population structure, the 52 accessions of the TCWTPC were classified into three major groups. Although most accessions of the TCWTPC were relatively clearly distinguished, SSR markers failed to distinguish several accessions belonging to the two weedy types of the crop. By using an association mapping analysis (AMA) of the 28 SSR markers and seven morphological characteristics in the 52 TCWTPC accessions, we detected that three of the SSR markers (KNUPF134, KNUPF137, KNUPF149) were associated with plant and seed characteristics. The novel SSR primer sets developed in crop should be useful in AMA for assessing genetic diversity and relationships between and within TCWTPC accessions, and this information will be helpful for genetic mapping in breeding programs for crop.