The present study reported the effectiveness of two PCR-based molecular techniques, inters simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs), for genetic assessment of amaranth. The polymorphic loci ranged from 110 among A. caudatus to 228 among A. cruentus and 16 among A. tricolor to 56 among A. hypochondriacus for AFLP primer combinations and ISSR primers, respectively. Among the two marker systems used, ISSR fingerprinting detected the highest number of alleles per locus (1.83) compared to AFLPs (1.63). However, the assay efficiency index for AFLP was 14.49, more than five-fold higher than ISSR (1.75). The study also revealed that ISSR primers with di-nucleotide repeats gave a good fingerprint, indicating that di-nucleotide repeats are more frequent in amaranth genome. The reproducibility of the two marker systems was confirmed by the narrow gene diversity (0.03 ± 0.11 to 0.07 ± 0.17) observed between the controls. Bayesian consensus and neighbor-joining trees were constructed to describe the cluster arrangement among the Amaranthus spp. The cluster pattern was similar for both markers, though the cluster order in the trees was slightly different. The results of this study confirm the usefulness of AFLPs and ISSRs for the genetic assessment of amaranth.