Abstract: The relationship between FST and canonical correlation analysis was revealed in this paper.The weakness of FST as a measurement of genetic differentiation among subpopulations was also indicated. The theoretical results demonstrate that multivariate statistical analysis is an effective method to study the distribution of population genetic variation. By using Canonical correlation analysis, we analyzed the data of 22 allozyme loci from 16 populations of Cunnlinghamia lanceoslata (Lamb.) Hook in People’s Republic of China.A detailed distribution pattern of gnentic variation was given, and greater differentiation among these populations was revealed.