Cadherin-6 (Cdh6) is a type II classic cadherin cell adhesion molecule whose expression delineates specific sets of rhombomeres during early mouse development. Here we establish a stable BAC transgenic mouse line in which enhanced green fluorescent protein (EGFP) recapitulates Cdh6 expression within the embryonic hindbrain. When the transgenic posterior hindbrain region at the embryonic (E) day 8.75-E9.75 that contains EGFP-positive rhombomere (r) 6-7 and EGFP-negative r4-5 cells was dissociated to single cells and incubated in suspensions, they were found to make aggregates only in the presence of calcium ion with the EGFP-Cdh6-positive/negative populations segregating each other in an aggregate. We further demonstrated that EGFP-Cdh6 expression boundary in the transgenic hindbrain at E9.5 shifted rostrally by the treatment that allows Hox gene expression anteriorize in the whole embryo culture system. These results suggest the role of Cdh6 in coordinating mouse hindbrain compartments possibly under the control of Hox gene regulatory network.