The discovery of avian cognitive abilities has revolutionised our understanding of the evolution of intelligence. However, the genetic basis of these abilities is unknown. One possibility is that numerous changes in genes across a wide range of functional domains are required for the evolution of complex intelligence. Alternatively, only a limited number of genetic tweaks might be required. Corvids are well known for their cognitive abilities such as episodic-like memory, problem solving, and tool use. The New Caledonian crow (Corvus moneduloides) is particularly intriguing as it is one of the few non-human species to manufacture foraging tools, making it an ideal model to study the genetic basis of cognition. Here we present genome-wide (~18,000 protein coding genes) phylogenetic comparisons among 12 crow species including C. moneduloides and scrutinize the genome for signatures of selection. In order to test whether similar genetic changes may have arisen earlier in the evolutionary history of the lineage, we perform the same analysis focusing on the closely-related tropical but non-tool using white-billed crow (Corvus woodfordi). We then use transcriptome data from C. woodfordi and avian protein databases to link candidate genes under selection to the species biology. We expect to detect signatures of positive selection (i.e. dN/dS >1) in genes associated with brain function and bill morphology allowing tool use and manufacture. Our results will help uncover the evolution and genetic basis of cognition in the wild and will reveal the nature of changes required to evolve cognitive abilities.