Auxin is a key phytohormone in plant somatic embryogenesis (SE) and YUCCA and AUXIN RESPONSE FACTORS (ARFs) are two key genes involved in auxin biosynthesis and auxin signaling pathways, respectively. They have been reported in participating to the catalytic production of endogenous indole-3-acetic acid (IAA; a natural auxin) and regulating the transcription of auxin-responsive genes. To explore the structural characteristics of the YUCCA and ARF families of Lilium spp. L. and its expression pattern during SE induction and development processes, 6 YUCCA genes and 12 ARF genes were screened from the transcriptome database, and their nucleotides and encoded proteins were analyzed. At the same time, the expression patterns of YUCCA and ARF genes were analyzed by reverse transcription quantitative PCR, and endogenous IAA content was measured. Results show that the members of Lilium indole-3-pyruvate monooxygenase YUCCA (LiYUCs) are structurally conserved among Lilium spp., Oryza sativa, and Arabidopsis thaliana. The LiARFs are classified into six groups, most LiARFs have a closer affinity to the monocotyledon Oryza sativa. All the 12 LiARFs are involved in the SE induction and development, but their expression patterns differed. The LiYUC2/4 and LiARF5/7/21 had expression profiles corresponding with IAA content during the SE induction periods. The LiYUC4/10 and LiARF7/17/18/20/21/22 showed a similar downward trend with IAA content during the progress of the SE development. The results provide a basis for further research on the functions of YUCCA and ARF genes during somatic embryogenesis of Lilium spp.