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The figwort genus <i>Scrophularia</i> L. (Scrophulariaceae) comprises 200-300 species and is widespread throughout the temperate Northern Hemisphere. Due to reticulate evolution resulting from hybridization and polyploidization, the taxonomy and phylogeny of <i>Scrophularia</i> is notoriously challenging. Here we report the complete chloroplast (cp) genome sequences of <i>S. henryi</i> Hemsl. and <i>S. dentata</i> Royle ex Benth. and compare them with those of <i>S. takesimensis</i> Nakai and <i>S. buergeriana</i> Miq. The <i>Scrophularia</i> cp genomes ranged from 152 425 to 153 631 bp in length. Each cp genome contained 113 unigenes, consisting of 78 protein-coding genes, 31 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, gene content, AT content and IR/SC boundary structure were nearly identical among them. Nine cpDNA markers (<i>trnH-psbA</i>, <i>rps15</i>, <i>rps18-rpl20</i>, <i>rpl32-trnL</i>, <i>trnS-trnG</i>, <i>ycf15-trnL</i>, <i>rps4-trnT</i>, <i>ndhF-rpl32</i>, and <i>rps16-trnQ</i>) with more than 2% variable sites were identified. Our phylogenetic analyses including 55 genera from Lamiales strongly supported a sister relationship between ((Bignoniaceae + Verbenaceae) + Pedaliaceae) and (Acanthaceae + Lentibulariaceae). Within Scrophulariaceae, a topology of (<i>S. dentata</i> + (<i>S. takesimensis</i> + (<i>S. buergeriana</i> + <i>S. henryi</i>))) was strongly supported. The crown age of Lamiales was estimated to be 85.1 Ma (95% highest posterior density, 70.6-99.8 Ma). The higher core Lamiales originated at 65.6 Ma (95% highest posterior density, 51.4-79.4 Ma), with a subsequent radiation that occurred in the Paleocene (between 55.4 and 62.3 Ma) and gave birth to the diversified families. Our study provides a robust phylogeny and a temporal framework for further investigation of the evolution of Lamiales.