The purpose of this research is to cluster and identify forty-one Camellia varieties by Fourier Transform Infrared (FTIR) spectroscopy of genomic DNA. We discovered FTIR spectra of genomic DNA are different among forty-one varieties tested. FTIR spectra can therefore act as a fingerprint for Camellia. Anova confirmed that the differences among FTIR data are significant. We set up the standard clustering and identifying model of forty-one Camellia varieties by hierarchical cluster combined with principal component analysis. The accuracy rate of clustering by using average spectra from one hundred and twenty-three genomic DNA samples is 92.68%. The identification accuracy rate is 100%. Clustering results showed that the forty-one Camellia varieties fall into nine categories based on a 1.0 cluster distance limit, and into three bigger categories at a 15.0 cluster distance limit. The genetic relationship analysis illustrates that the current Chuxiong population of C. reticulata Lindl. comes from Chuxiong, Tengchong, and Dali. We concluded that hierarchical clustering combined with principal component analysis based on FTIR spectra of genomic DNA can be used to quickly cluster and identify Camellia.