Herbicide-resistant (R biotype) and -sensitive (S biotype) individuals were identified from the same population, and seed was increased for each biotype for three generations. We conducted laboratory experiments to determine the effects of temperature, light, salt stress, osmotic stress, pH, and burial depth on the germination and emergence of resistant and sensitive biotypes of Japanese foxtail. The results revealed that there was no difference in the final germination rate between the two biotypes under different temperature conditions, but time to obtain 50% germination or emergence (tE50) and mean germination time of the R biotype were higher than that of the S biotype at 10 C and 15/10 C 12-h day/night regime. In dark conditions, the final germination rate of the S biotype was higher and lower than that of the R biotype at 10 and 25 C, respectively. The overall germination rate of the R biotype was lower than that in the S biotype, and extended germination time was required in extreme conditions, such as 250 mM NaCl and −0.4 MPa osmotic potential. The change in environmental pH had no effect on the germination of the two biotypes. Emergence of the R biotype was lower than the S biotype when seed was buried at least 8 cm deep in an organic matter substrate. This study demonstrated the pleiotropic effects of a resistance allele on seed germination and emergence under different environmental conditions. Deep tillage could be used to reduce the growth and spread of resistant Japanese foxtail individuals.