In our current global community with the rapid movement of products and people across and between continents, the emergence of a human pathogen can have devastating consequences. One dramatic example of this has been the emergence of Chikungunya virus (CHIKV), which causes a severe, prolonged, and debilitating arthralgic disease. This virus emerged in a large outbreak on the east coast of Africa in 2004; over the subsequent seven years, CHIKV has spread across the Indian Ocean, the Indian subcontinent, Southeast Asia and even reached Europe, leaving more than two million people affected. Because CHIKV has a small genome, currently available tools to analyze complete viral genomes have provided scientists with unique opportunities to understand the epidemiology, pathogenesis and transmission of the virus. The most commonly used application of these cutting edge tools has been to track the movement of the virus over time and space. While this is an important concept for identifying areas that remain at risk for outbreaks, these postgenomic era tools can also be applied to the highly significant tasks of understanding how viral microevolutionary changes can affect both invertebrate transmission and vertebrate virulence. Significant alterations in the patterns of CHIKV movement have already been identified using microevolutionary studies. These approaches now need to be further expanded to aid in expanding vaccine, therapeutic and control options. This review will highlight some of the most significant recent research developments obtained using these cutting edge approaches for CHIKV.