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Auxin transport mediates the asymmetric distribution of auxin that determines the fate of cell development. <i>Agrobacterium</i>-mediated genetic transformation is an important technical means to study gene function. Our previous study showed that the expression levels of <i>LpABCB21</i> and <i>LpPILS7</i> are significantly up-regulated in the somatic embryogenesis (SE) of <i>Lilium pumilum</i> DC. Fisch. (<i>L. pumilum</i>), but the functions of both genes remain unclear. Here, the genetic transformation technology previously developed by our team based on the <i>L.</i><i>pumilum</i> system was improved, and the genetic transformation efficiency increased by 5.7–13.0%. Use of overexpression and CRISPR/Cas9 technology produced three overexpression and seven mutant lines of <i>LpABCB21</i>, and seven overexpression and six mutant lines of <i>LpPILS7</i>. Analysis of the differences in somatic embryo induction of transgenic lines confirmed that <i>LpABCB21</i> regulates the early formation of the somatic embryo; however, excessive expression level of <i>LpABCB21</i> inhibits somatic embryo induction efficiency. <i>LpPILS7</i> mainly regulates somatic embryo induction efficiency. This study provides a more efficient method of genetic transformation of <i>L. pumilum</i>. <i>LpABCB21</i> and <i>LpPILS7</i> are confirmed to have important regulatory roles in <i>L. pumilum</i> SE thus laying the foundation for subsequent studies of the molecular mechanism of <i>Lilium</i> SE.