Chromosomal polymorphisms such as inversions have been linked to the evolution of phenotypic variation, environmental adaptation, and speciation. Recombination suppression within such polymorphisms leads to genetic divergence between the two chromosome types and can enable the evolution of coadapted alleles. The genome of the white-throated sparrow (Z. albicolis) contains two exceptionally large chromosomal polymorphisms. The rearrangement on the 2nd chromosome (ZAL2/2^m) has been the subject of extensive study and is linked to both plumage morph and alternative reproductive strategies. Here, we describe our early investigations of a polymorphism on the 3rd chromosome (ZAL3/3^a). Using whole-genome sequencing data, we estimate that the ZAL3 rearrangement is larger in physical size compared to the ZAL2 rearrangement, capturing nearly 1000 genes, but shows less genetic divergence between the two haplotypes. Fixed differences between the haplotypes are predicted to disrupt the coding sequences of several genes, as well as the regulatory sequences of many more. We analyzed both gene expression and allelic bias in brain, heart, and liver tissues, uncovering evidence of regulatory variation on ZAL3 with probable phenotypic effects. By genotyping hundreds of archived samples, we found that ZAL3^a/3^a is the most common genotype (77% of samples), followed by ZAL3/3^a (21%), and ZAL3/3 (2%). The frequencies of each ZAL3 genotype varied by sex, plumage morph, and year, and ZAL3/3 homozygotes had poorer body condition. These findings provide the first evidence of genetic divergence resulting from the ZAL3 polymorphism and its functional consequences.