To reveal the genetic properties of an Afghan wheat collection maintained in Kyoto University, variations in morphological character and HMW glutenin subunit composition were investigated in 410 Afghan wheat accessions together with 65 accessions of Iranian and Pakistani wheat. The majority of the samples had primitive morphological characteristics, namely, tall plant height and lax spikes with a spelt head. The most frequent combination of HMW glutenin subunit was Glu-A1c (encoding subunit null), Glu-B1b (7 + 8), and Glu-D1a (2 + 12). Alleles preferable for modern breeding such as Glu-B1c and Glu-D1d were rare in our samples. Consequently, we concluded that the Afghan wheat accessions investigated in this study have genetic characteristics typical of landraces. As for their genetic diversity, the level of variation in the HMW glutenin subunit in Afghanistan was found to be equal to or lower than that in the neighboring countries. The largest variation was observed in Western Iran and Pakistan. AFLP analysis using 91 representative accessions also showed a comparatively low level of diversity in Afghanistan. These results suggest that a decrease in genetic diversity has occurred in Afghanistan. A novel HMW glutenin subunit (2.8) was found in this study, indicating the potential usefulness of Afghan landraces for wheat breeding.