Chromosome rearrangements such as inversions have been recognized previously as contributing to reproductive isolation by maintaining alleles together that jointly contribute to deleterious genetic interactions and postzygotic reproductive isolation. In this study an impact of potential incompatibilities merely residing on the same chromosome is found in crosses of populations of the copepod Tigriopus californicus. When genetically divergent populations of this copepod are crossed, hybrids show reduced fitness and deviations from expected genotypic ratios can be used to determine regions of the genome involved in deleterious interactions. In this study a set of markers is genotyped for a cross of two populations of T. californicus and these markers show widespread deviations from Mendelian expectations with entire chromosomes showing marked skew. Despite the importance of mtDNA/nuclear interactions in incompatibilities in this system in previous studies, in these crosses the expected patterns stemming from these interactions are not widely apparent. Females lack recombination in this species and a striking difference is observed between male and female backcrosses. This suggests that the maintenance of multiple loci on individual chromosomes can enable some incompatibilities, perhaps playing a similar role in the initial rounds of hybridization to chromosomal rearrangements in preserving sets of alleles together that contribute to incompatibilities. Finally, it is observed that candidate pairs of incompatibility regions are not consistently interacting across replicates or subsets of these crosses despite the repeatability of the deviations at many of the single loci themselves, suggesting that more complicated models of Dobzhansky-Muller incompatibilities may need to be considered.