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The first complete chloroplast genome sequences of new intercepted alien weeds in China, pentandra (L.) C. Jeffrey, were reported in this study. The Z. pentandra plastome was 153,239 bp long, with the large single copy (LSC) region of 83,528 bp, the small single copy (SSC) region of 18,081 bp, and two inverted repeat (IR) regions of 25,815 bp. The plastome contained 130 genes, including 85 protein-coding, 8 ribosomal RNA, and 37 transfer RNA genes. The overall GC content was 37.0%. Phylogenetic analysis of 32 representative plastomes within the family Aizoaceae suggests that Zaleya is more closely related to Tetragonia than to Sesuvium which is different previous studies. However, due to the limited chloroplast genome accessions in Aizoaceae at present, the phylogenetic relationship between the subfamilies of the family cannot be further discussed.