TBX1 is a major disease gene of 22q11.2 deletion syndrome (22q11.2DS). It is expressed in all three germ layers of pharyngeal apparatus to control the complicated morphogenesis. The haploinsufficiency of pharyngeal endodermal or ectodermal, but not mesodermal Tbx1 causes aortic arch patterning defect. However, the mesodermal deletion of Tbx1 causes much severer pharyngeal and cardiovascular defect than either pharyngeal endodermal or ectodermal Tbx1 deletion does. It is inconsistent with the conventional thought that the invagination of pharyngeal epithelia drives pharyngeal segmentation. Therefore, we asked whether pharyngeal ectodermal and ectodermal Tbx1 can compensate the loss of each other. Here we carefully characterized pharyngeal epithelia-specific Fgf15Cre and Fgf15HspCre lines and used them to perform pharyngeal epithelia-specific deletion. Our data showed that the percentage of E18.5 Fgf15Cre;Tbx1flox/thorn embryos with aortic arch patterning defects was similar to that of E10.5 Fgf15Cre;Tbx1flox/thorn embryos with the 4th pharyngeal arch artery (PAA) defect, indicating that there is no significant recovery from the initial PAA defect, in contrast to germ line haploinsufficiency. Fgf15Cre;Tbx1flox/flox embryos had hypoplastic caudal pharyngeal arch and defective derivatives, but cardiac OFT development was not affected. The phenotypic spectrum of simultaneous Tbx1 deletion in both pharyngeal ectoderm and endoderm is strikingly similar to what presents with single pharyngeal endoderm or ectoderm-specific deletion of Tbx1. The absence of synergistic effect indicates intimate topographic interactions among pharyngeal endoderm and ectoderm, through which deletion of a gene in one tissue may disrupt the development of adjacent tissues and thereby lead to similar morphological phenotypes in either tissue-specific deletion. (C) 2020 Elsevier Inc. All rights reserved.