Chenopodium quinoa Wild. and Amaranthus caudatus L., two plant species from South America, have small and numerous chromosomes. Looking for chromosome markers to distinguish pairs of homologous chromosomes double fluorescence staining, in situ hybridization with 45S rDNA and silver staining were applied. Fluorescent in situ hybridization with 45S rDNA has shown two sites of hybridization occurring on one pair of chromosomes in quinua genome (lines PQ-1, PQ-8). The number of rDNA loci in Amaranthus caudatus L. genome depends on the accession. Kiwicha 3 line has one pair of chromosomes with signals and Kiwicha Molinera cultivar two pairs. All observed rDNA loci were active. After chromomycin/DAPI staining in all cases, except Kiwicha Molinera cultivar, the CMA3 positive bands co-localized with signals of in situ hybridization with rDNA. In Kiwicha Molinera the number of CMA+bands was higher than the number of 45S rDNA signals after FISH.