Phylogenetic analysis of plastid encoded ndhF coding sequences for the Chenopodiaceae-Amaranthaceae alliance reveals a monophyletic Chenopodiaceae-Amaranthaceae clade sister to Achatocarpaceae. The Chenopodiaceae-Amaranthaceae-Achatocarpaceae clade is in turn sister to the Caryophyllaceae, the Chenopodiaceae-Amaranthaceae-Achatocarpaceae-Caryophyllaceae clade forming a separate lineage within order Caryophyllales. The Chenopodiaceae as currently circumscribed is paraphyletic and the alliance breaks into a polytomy of four major clades: (i) Amaranthaceae-Polycnemoideae, (ii) Chenopodieae-Atripliceae, (iii) SalicornioideaeSalsoloideae, and (iv) Beteae. Character-state optimizations of morphological characters mapped onto ndhF sequence derived phylogenies reveal phylogenetically significant patterns of character-state distribution. Morphological investigations also revealed a previously undetected branching pattern in the Gomphrenoideae, which is here described, illustrated, and discussed. Morphological analyses of Amaranthus led to the discovery of a previously undescribed species, which is here described and illustrated and its morphological affinities discussed.