Currently, there is no economical way to produce large quantities of F1 hybrid soybean seed in the USA. One of the fundamental requirements for hybrid seed production is the availability of a stable male-sterile, female-fertile system. However, the more challenging barrier is the efficient transfer of pollen from the male parent to the female parent. This could potentially be achieved through pollinator insects. Our observations suggested that seed set on male-sterile, female-fertile plants is a good indicator of insect attraction. The objective of this study was to evaluate seed set among male-sterile, female-fertile lines segregating for male-sterile, female-fertile ms6 allele by using Megachile rotundata as pollinator vector. Thirty-four pairs of near-isogenic lines, the ms6 w1w1 donor parent, and its two isogenic lines W1w1 and w1w1 segregating for male-sterile (ms6) allele were used. The W1 locus controls flower color and hypocotyle pigmentation. Seed set was evaluated on field-grown plants in 2001–2003 near Ames, IA. Although the observed seed set was not commercially acceptable, our results indicated significant differences in seed set among lines. This suggests that preferential attraction of pollinators occurred, and selection among male-sterile, female-fertile lines could be used to obtain female parents suitable to produce larger amounts of hybrid soybean seed. In addition, the effect of flower color on seed set was statistically significant. White-flowered lines (w1w1) produced more seed set compared to purple-flowered lines (W1W1). Lastly, the important effect of year suggested that the effect of environmental conditions on seed set among lines segregating for male sterility was of paramount importance to plant–pollinator interactions. This needs to be assessed in order to establish an efficient hybrid soybean program