The vertebrate hindbrain is segmented into an array of rhombomeres (r), but it remains to be fully understood how segmentation is achieved. Here we report that reducing meis function transforms the caudal hindbrain to an r4-like fate, and we exploit this experimental state to explore how r4 versus r5-r6 segments are set aside. We demonstrate that r4 transformation of the caudal hindbrain is mediated by paralog group 1 (PG1) hox genes and can be repressed by vhnf1, a gene expressed in r5-r6. We further find that vhnf1 expression is regulated by PG1 hox genes in a meis-dependent manner. This implies that PG1 hox genes not only induce r4 fates throughout the caudal hindbrain, but also induce expression of vhnf1, which then represses r4 fates in the future r5-r6. Our results further indicate that r4 transformation of the caudal hindbrain occurs at intermediate levels of meis function, while extensive removal of meis function produces a hindbrain completely devoid of segments, suggesting that different hox-dependent processes may have distinct meis requirements. Notably, reductions in the function of another Hox cofactor, pbx, have not been reported to transform the caudal hindbrain, suggesting that Meis and Pbx proteins may also function differently in their roles as Hox cofactors.