Abstract: The genus, Amaranthus, is a typical annual flowering plant valued as vegetables, grains and ornamentals. It exhibits a high degree of interspecies variability and as such enhances biodiversity. Two common grain types (A. caudatus and A. cruentus) and three major weedy types (A. hybridus, A. spinosus and A. viridis) were studied. Phenotypic traits were determined using FAO descriptors for both qualitative and quantitative traits. Extracted DNA samples were amplified through the PCR technique using four RAPD primers (OPA-02, OPA-04, OPB-08 and OPE-01). Statistical analyses for morphological and molecular data were done using the NTSYS Version 2.02j software. Qualitative morphological characters did not significantly discriminate among the five species except for floral morphology. Quantitative characters, however, exhibited wide interspecies variation. Morphological cluster analysis showed that the five species were entirely distinct with a similarity coefficient of 0 except for A. cruentus and A. hybridus which shared an even very low coefficient of 0.093. The RAPD primers generated a total of 150 bands in the size range of 250-2000 bp. Molecular cluster analysis showed that all the species studied shared a similarity coefficient of 0.57 and some individuals within each species were clustered with individuals from other species. For example, most of the randomly selected plants from A. viridis were clustered with plants selected from A. spinosus at a similarity coefficient up to 0.81. This close relationship between A. viridis and A. spinosus may be of medicinal importance for both humans and animals especially since A. viridis is more appealing for consumption. The use of RAPD molecular marker systems in Amaranthus spp. should be advanced so as to impel specific linkage among genes controlling important traits.