Alloplasmic lines or cytoplasmic substitution lines of bread wheat (Triticum aestivum) that have cytoplasm from a related wild Aegilops species through recurrent backcrossing exhibit several useful characteristics for wheat breeding. Using an alloplasmic line initially developed by Professor Tsunewaki, we derived new alloplasmic lines for 14 Japanese bread wheat cultivars with Aegilops mutica cytoplasm to examine the effects of the cytoplasm on agronomic characters. All alloplasmic lines showed delayed heading time (4 to 17 days in the field) compared with the euplasmic lines, and the degree of heading delay depended on VERNALIZATION1 (VRN1) genotype. In spring wheat cultivars such as ʻMinaminokaoriʼ that carry the dominant VRN-A1 allele, the degree of heading delay due to the alien cytoplasm was large; by contrast, in winter wheat cultivars such as ʻHaruibukiʼ that carry recessive vrn1 alleles in three homoeologous genes, the heading delay was small. Compared with euplasmic lines, the alloplasmic lines generally showed increased spikelet number per spike, but decreased floret number per spikelet, leading to decreased grain number per spike (GNS). However, GNS varied depending on genotype; in the alloplasmic lines of ʻNanbukomugi,ʼ ʻNebarigoshi,ʼ and ʻFukusayaka,ʼ no decrease in GNS occurred. Furthermore, the ʻNebarigoshiʼ and ʻFukusayakaʼ alloplasmic lines could suppress the decrease in spike number per plant during winter due to delayed flowering. These alloplasmic lines will be useful for the development of varieties adapted to global warming.