Since clear identification of individual chromosomes in Capsicum species was not possible due to the gradient in sizes and similar morphology, in situ hybridization using 5S rDNA and 18S-26S rDNA probes was utilized to karyotype the chromosomes of the five species, Capsicum annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens. The 5S rDNA located on only one pair of chromosomes in all five species. The 5S rDNA carrying chromosome was designated as chromosome 1 by the synteny relationship with tomato. In two species, C. baccatum and C. pubescens, the 5S rDNA was physically linked with a 18S-26S rDNA locus. The number and chromosomal location of 18S-26S rDNA loci were highly variable among the species. The number of loci was as few as two in C. annuum and as many as 14 in C. baccatum. The chromosomal positions of the 18S-26S loci were in the telomere regions in the corresponding chromosomes and some chromosomes showed hybridization signals in this region of both long and short arms. A pair of acrocentric chromosomes carrying the 18S-26S rDNA locus in the satellite region was found in all five species. The in situ and Southern hybridization patterns of the rDNAs were similar between C. annuum and C. chinense. C. frutescens was similar to C. chinense. C. baccatum and C. pubescens were speculated to be less related to the former three Capsicum species. The variable nature of the 18S-26S rDNA loci in the Capsicum species might provide a good model for rDNA evolution.