Vaccinium darrowi (D) is a wild blueberry species with low chilling requirements for budbreak, and heat and drought tolerance. Breeding efforts to incorporate these desirable traits into cultivated blueberry (V. corymbosum) (C) would be facilitated with a better understanding of the genomic homology between the two species. An interspecific tetraploid hybrid (CCDD, 2n=4x=48) was used to evaluate genome homology and interspecific recombination. Pollen mother cells examined at diakinesis and early metaphase I exhibited an average of 4.6 chain bivalents, 11.4 ring bivalents, 1.0 chain quadrivalent, and 3.0 ring quadrivalents. This data most closely fits a chromosome pairing model in which there is a greater pairing affinity between homologues than homoeologues. An analysis of the inheritance of 14 RAPD markers unique to V. darrowi in 72 backcross progeny of the V. darrowi–corymbosum hybrid also supported the pairing model: Seven of the 14 markers deviated significantly from tetrasomic inheritance ratios, expected if chromosome pairing was totally random. On the basis of the cytogenetic and RAPD analyses, the genomes of V. darrowi and V. corymbosum are divergent from one another, with preferential pairing within genomes. This outcome suggests there may be difficulty in breaking undesirable linkages when introgressing desirable traits from V. darrowi to V. corymbosum.