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Amaranthus is one of the underutilized species distributed and utilized worldwide. In the study was used ISSR approach to analyse intra and inter-specific variability of 16 Amarathus caudatus, 19 A. cruentus and 21 A. hypochodriacus accessions. Using of 11 ISSR primers, fragments levels ranged from 15 up to the 24 were obtained. In the dendrogram based on ISSR data set individual species separation is observed except of three accessions. Two A. caudatus genotypes originated from India clustered with A. hypochondriacus accessions and one A. hypochondriacus genotype originated from Nepal clustered with A. cruentus accessions. Average similarity index among all 55 analysed genotypes ranged from 0,154 to 1,000 with a mean of 0,522. Highest intaspecific variability is reported for A. hypochondriacus accessions when comparing to the A. caudatus or A. cruentus. This study has demonstared, that a single primer marker system as ISSR is able to generate a sufficient level of informative characters for intra and inter-specific molecular analysis of Amaranthus genus. [ABSTRACT FROM AUTHOR]