We present a new method for ascertaining the rate of nucleotide substitution between subtypes and apply this method together with traditional MCA methods to date the divergence of influenza subtypes A-H3N2, B, and C. We use three genes, HA, MP and NS, to date two types of divergence events: the time of the most recent common of each subtype and the time of divergence between two subtypes, A-H3N2 and B. For the former event type, we show that the three genes are loosely consistent in their dating of the TMRCA of the subtypes, with the notable exception of the HA-derived estimate of subtype C's TMRCA approximately 50 years before the MP-and NS-derived estimates. This discrepancy may indicate either that subtype C's hemagglutinin-esterase gene engaged in a biologically significant event, such as reassortment, or that MCA estimation does not adequately model the evolution of the gene.