Whole genome duplication (WGD) generates a new genetic material that can contribute to the evolution of developmental processes and phenotypic diversification. A WGD occurred in an ancestor of arachnopulmonates (spiders, scorpions, and their relatives), which provides an important independent comparison to WGDs in other animal lineages. After WGD, arachnopulmonates retained many duplicated copies (ohnologues) of developmental genes including clusters of homeobox genes, many of which have been inferred to have undergone subfunctionalization. However, there has been little systematic analysis of gene regulatory sequences and comparison of the expression of ohnologues versus their single-copy orthologues between arachnids. Here, we compare the regions of accessible chromatin and gene expression of ohnologues and single-copy genes during three embryonic stages between an arachnopulmonate arachnid, the spider Parasteatoda tepidariorum, and a nonarachnopulmonate arachnid, the harvestman Phalangium opilio. We found that the expression of each spider ohnologue was lower than their single-copy orthologues in the harvestman suggesting subfunctionalization. However, this was not reflected in a reduction in the number of peaks of accessible chromatin because both spider ohnologues and single-copy genes had more peaks than the orthologous harvestman genes. We also found that the number of peaks of accessible chromatin was higher in the late embryonic stage associated with activation of genes expressed later during embryogenesis in both species. Taken together, our study provides a genome-wide comparison of gene regulatory sequences and embryonic gene expression in arachnids and thus new insights into the impact of the arachnopulmonate WGD.