Amaranthus, a genus in Amaranthaceae, is divided into three subgenera—Amaranthus, Acnida, and Albersia—and contains approximately 70 to 80 species. Understanding its phylogenetic relationships is essential for species classification, genetic diversity assessment, and evolutionary studies. This knowledge is vital for improving Amaranthus utilization in crop improvement and managing the ecological impacts of invasive weeds. In this study, we analyzed the chloroplast genomes of 27 Amaranthus species across all three subgenera to characterize their genomic features and construct a comprehensive phylogenetic tree. Our aim was to elucidate the phylogenetic relationships within the genus and evaluate interspecific affinities among the subgenera. We also addressed the taxonomic ambiguity surrounding A. bouchonii and A. powellii to determine their distinct species within the genus. Chloroplast genome sizes ranged from 149,949 to 150,818 bp, with GC content varying between 36.52% and 36.63%. Comparative structural analyses confirmed highly conserved quadripartite structures, gene content, and organization, comprising 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat and codon usage analyses revealed conserved repeat patterns and a preference for codons ending in A or U. Selection pressure analysis indicated a predominantly purifying selection, with matK showing signs of positive selection, particularly in A. spinosus. Phylogenetic analysis of 80 protein-coding genes confirmed the monophyly of subgenus Amaranthus but found Alberisa and Acnida to be paraphyletic. Despite their morphological similarity, A. bouchonii and A. powellii were placed in separate clades within subgenus Amaranthus, with A. bouchonii clustering with A. retroflexus, and A. powellii aligning with the A. hybridus complex. Additionally, we identified 16 variable regions as potential molecular markers for species identification. Our study provides the most comprehensive Amaranthus chloroplast genome dataset to date, offering new insights into its evolutionary relationships and valuable genomic resources for taxonomy, germplasm management, and invasive risk assessment.

Two new species of Salvia zayuensis and S. toxantha (Lamiaceae), from Southwest China, are described. Salvia zayuensis is similar to S. cyclostegia but is distinguished by its larger cauline leaves (18.2–24.0 cm), densely hoary appressed trichomes on young rachises and abaxial leaf and bract surfaces, and peach-shaped juvenile inflorescences maturing into 40 cm long. Its corolla is bicolored (purplish-brown upper lip, yellow lower lip) with the anther connective 0.15 cm shorter in arc length. Salvia toxantha resembles S. smithii in leaf shape, inflorescence structure, bract and bracteole morphology, and corolla color, yet it is characterized by the absence of lemon scent, longer pedicels and calyxes, a slender, bow-shaped corolla, and purple-brown spots on the middle lobe of lower lip. Additionally, its anther connective is ca. 0.4 cm shorter than that in S. smithii . Phylogenetic analysis of chloroplast genome places both new species within the subclade Eurysphace of subg. Glutinaria .