Herbicide-resistant wheat cultivars are an effective tool in controlling weeds. The CoAxium wheat (Triticum aestivum L.) cultivar conferring tolerance to quizalofopp-ethyl herbicide was developed along with a bioassay to quantify traited seeds in a sample. The objectives of this study were to (1) compare a current seed soaking (SS) method with substrate imbibition (SI) method in detecting AXigen trait in two genotypes, CO14A050 (homozygous resistant-A/D genomes) and CO14A136 (homozygous resistant-B/D genomes), and (2) develop criteria to distinguish between trait and nontrait seedlings based on chemical injury using standard germination, linear length, and dry matter content tests. Quizalofop doses 0.0, 3.0, 4.0, and 5.0 μM were used in both methods. A soft white winter wheat, Bobtail, was used as a susceptible control. Using SS, 96% of Bobtail seedlings were classified as nontrait at 3.0 μM and 100% at 4.0 and 5.0 μM; however, using SI, only 1.0%-6.0% showed chemical injury and were classified as nontrait. The SI did not differentiate between trait and nontrait seedlings at any dose. At 5 μM, CO14A136 showed significant chemical injury (26%) compared to CO14A050 (1%). A greenhouse dose-response study confirmed that CO14A136 conferred lower tolerance to quizalofop than CO14A050. The SS method at 5 μM was suitable for identifying trait and nontrait seeds. It is recommended that both root and shoot structure should be considered in evaluating trait and nontrait seedlings, not only roots like the current protocol.