The thymus is a conserved organ among vertebrates, derived from the endoderm of distinct pharyngeal pouches (PP), whose location and number vary in different species. Together with reports of sporadic ectopic thymus locations in mice and humans, this suggests that the potential to make a thymus resides in a broader region of the PP endoderm than previously ascribed. Using the chick-quail chimera system, we explore this hypothesis and test the capacity of non-canonical pouches to participate in thymus formation. We further ask if the local mesenchyme of pharyngeal arches (PA) could also play a role in the regulation of thymus formation. After testing several embryonic tissue associations, we mapped the pharyngeal endoderm regions with thymus potential to the second and third/fourth pharyngeal pouches (2PP and 3/4PP). We further identified mesenchyme regions that regulate this potential to the the 3/4 pharyngeal arches and to the dorsal region of the second arch, with positive and negative influences, respectively. Transcriptomic analysis of these tissues helped us to delineate a common genetic program correlated with thymus potential in the endoderm, and to define distinct signalling pathways acting in mesenchymal environments to help patterning pharyngeal arches. Together, these results provide new information about the initial specification of thymus primordia in the embryo and might help in improving thymus organoid systems.