Most of Chinese chive (Allium ramosum L.; A. tuberosum Rottl. ex Spr., synonym) cultivars are autotetraploid. Because they exhibit a high degree of apomixis, cross breeding of this crop has not been developed yet. In this study, we crossed an amphimictic diploid accession of Chinese chive, 94Mo49, with an accession of A. scabriscapum Bois. et Ky., RAR930068, a wild species, to investigate the possibility of using the wild species as a genetic resource for Chinese chive cross breeding. Pollen and seed fertility of the parental species and F1 hybrids (A. ramosum × A. scabriscapum) was investigated. Hybrid confirmation of reciprocal F1 hybrids was conducted by PCR analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA). In fertility tests, both of A. ramosum and A. scabriscapum accessions showed high pollen fertility (> 94%), whereas the F1 hybrids showed pollen sterility. Although seed set percentages in reciprocal crossings were nearly equal, the germination rate of seeds from A. scabriscapum was much lower than that of seeds from A. ramosum. Although F1 hybrids exhibited low seed sets (< 10%), they could produce BC1 (F1 hybrids × A. ramosum) seeds with relatively high germination rates. In the analysis of ITS region of nrDNA, reciprocal F1 hybrids possessed both specific fragments from A. ramosum and A. scabriscapum, which confirmed their hybridity. Our results confirmed that A. scabriscapum was useful for Chinese chive breeding as a secondary gene pool.