Zoysia matrella (L.) Merr. is a homoploid turfgrass that possesses intermediate traits between Z. japonica Steudel and Z. pacifica (Goudswaard) M. Hotta and Kuroki [syn. Z. matrella (L.) Merr. var. pacifica Goudswaard]. Consequently, it contributes to the growing range of variation that exists within this species. Self‐pollination reduces genetic load and can express genetic variance, enabling easy identification and selection for desired traits. The aim of this study was to evaluate the effects of self‐pollination of Z. matrella ‘Wakaba’ on morphological traits, genetic structure, and the possible selection of lines with superior traits in S1 progeny. Nine morphological characteristics (plant height, leaf width and length, stolon diameter and internode length, inflorescence number, ground covering, normalized difference vegetation index, and leaf color) were evaluated in the 364 S1 progeny. We have obtained S1 progeny exhibiting wide variation in morphological characteristics and moderate inbreeding depression in almost all traits after self‐pollination. To infer genetic structure, a total of 26 simple sequence repeat markers were used, and Bayesian‐based structure analysis grouped the progeny into three clusters. Genetic markers revealed that the level of homozygosity increased in S1 progeny caused by inbreeding. Superior progeny that exhibited high ground covering, late winter dormancy, and stay green throughout the entire winter season were selected. Self‐pollination can be used for the selection of desirable traits from highly heterozygous species such as Z. matrella. Moreover, we expect that these superior progeny could be used in further study on quantitative trait loci analysis.