Amaranthus (Amaranthaceae) is a globally distributed plant genus composed of both weedy and cultivated species. While there have been previous attempts to resolve phylogenetic relationships within the genus, little attention has been placed on systematic relationships of the federally threatened coastal species Amaranthus pumilus Raf., endemic to eastern United States barrier islands, nor on genetic variability within the genus. In the present study, single primer ISSRs were employed to measure both genetic diversity and the phylogenetic position of A. pumilus. Leaf tissue samples were taken from wild populations on Fenwick Island, Delaware and from wild and propagated populations on Assateague Island National Seashore, Maryland. Genetic variation was detected among and within A. pumilus populations, though variability was low. Fenwick populations exhibited the highest genetic variability (h  =  0.1016), while on Assateague the wild A. pumilus population had higher variability (0.0340) than the propagated population (0.0185). Due to its desirable characteristics in plant breeding trials, genetic variation within A. pumilus was also compared to variation of grain varieties A. hypochondriacus L. and A. cruentus L. Genetic diversity within A. pumilus was lower than either grain species sampled (0.2263 and 0.2947). Phylogenetic analyses included 41 accessions representing 33 Amaranthus species, and maximum parsimony, neighbor-joining, and Bayesian consensus trees were constructed. Though considerable phylogenetic signal was detected within the data matrix, phylogenetic resolution was low. Amaranthus pumilus grouped with the coastal species A. arenicola I.M. Johnst. in all consensus trees, which is the first postulated relationship of this pair.