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Intragenomic variability is known to be present in multi-copy gene sequences of several plant species and causes severe problems on molecular phylogenetic analysis. Initial investigation revealed extensive presence of intragenomic variability in nrITS of Camellia. Detailed investigation using 20–30 sequences from each leaf sample of seven species of Camellia revealed considerable sequence variability in terms of Kimura pair-wise distance, nucleotide diversity and Tamura's D parameters. Fluorescence in situ hybridization (FISH) revealed the dispersion of rDNA loci into multiple chromosomes and a small percentage of species in Camellia were allotetraploids. The distribution of rDNA loci into nonhomologous chromosomes along with long generation period and incidence of the interspecific hybridization are considered the major reasons for the failure of complete homogenization of the nrITS repeats by concerted evolution in Camellia. Nevertheless, in the majority diploid species or in the dominant sequence types of the allotetraploids, nrITS sequence variability was not high enough to obliterate the phylogenetic signals. Thus, utilization of nrITS in the phylogeny of Camellia is still possible, if adequate care is taken.