Tbx1 is required for the expansion of second heart field (SHF) cardiac progenitors destined to the outflow tract of the heart. Loss of Tbx1 causes heart defects in humans and mice. We report a novel Tbx1(Cre) knock-in allele that we use to fate map Tbx1-expressing cells during development in conjunction with a reporter and 3D image reconstruction. Tbx1 descendants constitute a mesodermal cell population that surrounds the primitive pharynx and approaches the arterial pole of the heart from lateral and posterior, but not anterior directions. These cells populate most of the outflow tract with the exception of the anterior portion, thus identifying a population of the SHF of distinct origin. Both myocardial and underlying endocardial layers were labeled, suggesting a common origin of these cell types. Finally, we show that Tbx1(Cre)-positive and Tbx1(Cre)-negative cell descendants occupy discrete domains in the outflow tract throughout development.