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Summary Tfap2b, a pivotal transcription factor, plays critical roles within neural crest cells and their derived lineage. To unravel the intricate lineage dynamics and contribution of these Tfap2b+ cells during craniofacial development, we established aTfap2b‐CreER^T2knock‐in transgenic mouse line using the CRISPR‐Cas9‐mediated homologous direct repair. By breeding with tdTomato reporter mice and initiating Cre activity through tamoxifen induction at distinct developmental time points, we show theTfap2blineage within the key neural crest‐derived domains, such as the facial mesenchyme, midbrain, cerebellum, spinal cord, and limbs. Notably, the migratory neurons stemming from the dorsal root ganglia are visible subsequent to Cre activity initiated at E8.5. Intriguingly, Tfap2b+ cells, serving as the progenitors for limb development, show activity predominantly commencing at E10.5. Across the mouse craniofacial landscape, Tfap2b exhibits a widespread presence throughout the facial organs. Here we validate its role as a marker of progenitors in tooth development and have confirmed that this process initiates from E12.5. Our study not only validates theTfap2b‐CreER^T2transgenic line, but also provides a powerful tool for lineage tracing and genetic targeting ofTfap2b‐expressing cells and their progenitor in a temporally and spatially regulated manner during the intricate process of development and organogenesis.