We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets, (2) enabling creation and analyses of groups of sequences, (3) enabling specification of domains and genes, (4) expanding the repertoire of statistical methods for molecular evolutionary studies, and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform.