Rhombomeres appear transiently in the vertebrate hindbrain shortly after neurulation and are thought to represent embryologic compartments in which the expression of different combinations of genes leads to segment-specific differentiation of the developing hindbrain, the cranial ganglia, and the branchial arches. To determine the extent to which gene expression is related to the formation of visible rhombomere boundaries, we have examined, by in situ hybridization, the expression of five rhombomere-specific genes in mouse embryos homozygous for the kreisler (kr) mutation, in which rhombomeres 4–7 are replaced by a smooth morphologically unsegmented neural tube. Using molecular probes specific for Hoxb-1 (Hox-2.9), Hoxb-3 (Hox-2.7), Hoxb-4 (Hox-2.6), Krox-20, or Fgf-3 (Int-2), we found that the kr mutation affects the expression of all the genes we examined, but, surprisingly, the altered patterns of expression are not restricted to that portion of the mutant hindbrain which is morphologically abnormal. Rostral expression boundaries of Hoxb-3 and Hoxb-4 are displaced from their normal positions at r4/5 and r6/7 to the approximate positions of r3/4 and r4/5, respectively. The expression domains of Krox-20 and Fgf-3 are also displaced in a rostral direction and the intensity of Fgf-3 hybridization is greatly reduced. The expression domain of Hoxb-1 is affected differently from the other genes in kr/kr embryos; its rostral boundary at r3/4 is intact but the caudal boundary is displaced from its normal location at r4/5 to the approximate position of r5/6. Because boundaries of gene expression for Hoxb-1 and Hoxb-4 are found in a region of the kr/kr hindbrain that lacks visible rhombomeres, establishment of regional identity, as reflected by differential gene expression, does not require overt segmentation. To investigate whether the altered patterns of gene expression we observed in the kr/kr embryonic hindbrain are associated with morphologic changes in the adult, we examined neural crest-derived tissues of the second and third branchial arches, which normally arise from rhombomeres 4 and 6, respectively. We found that the hyoid bone in kr/kr animals exhibited an accessory process on the greater horn (a third arch structure) most easily explained by ectopic development of a second arch structure (the hyoid lesser horn) in an area normally derived from the third arch.