Genomics promises to answer both deep and shallow phylogenetic questions. Here, two spider problems are discussed: one involves the evolutionary origins of the Psechridae, an enigmatic group of lycosoid spiders in which traditional molecular systematics has repeatedly failed to recover its deeper relationships; the other involves the evolution of Metepeira in South America, in which traditional methods have failed to resolve the shallow relationship questions. In the first case, transcriptomics has succeeded in resolving the deeper relationships that were otherwise recalcitrant. The second case is an on-going project that has yet to be answered, but different phylogenomic options may prove suitable in this instance as well.