The recent discovery of a whole genome duplication (WGD) event in arachnids with book lungs (Arachnopulmonata) posits them as ideal research organisms to study the implications of this process in the evolution of morphology. A fascinating phenomenon that has independently evolved in different arachnid orders is the “antennification” of a walking leg pair to serve a sensory function, a convergence with the antenna of mandibulates (e.g., insects, centipedes). Arguably the most complex antenniform legs in arachnids occur in the arachnopulmonate order Amblypygi (whip spiders) but it is unknown if they retain ohnologs from the inferred WGD event, and which genetic factors specify the fate of antenniform legs. To investigate the incidence of systemic gene duplications in this order, we assembled the first embryonic transcriptomic resources for three whip spider species. We show evidence that Amblypygi retain two complete Hox clusters and duplicates of numerous developmental patterning genes. We then established an evo-devo tool kit for the species Phrynus marginemaculatus and showed that expression of leg gap gene paralogs (Distal-less, dachshund and homothorax) support a shared WGD across Arachnopulmonata. Next, we conducted differential gene expression analysis between antenniform legs and walking legs in embryonic stages before and after leg specification, revealing candidate genes with verifiable expression patterns via in situ hybridization. In particular, we found evidence that a Hox gene paralog may be involved in the early specification of the sensory leg, a hypothesis amenable to testing with the functional tools we have recently established for this species.