The Mendelian pea (Pisum sativa), a member of the Fabaceae family, is widely cultivated worldwide as an important food resource. While extensive genetic studies have been conducted on pea, a comprehensive pan-plastome assembly has not yet been achieved. The present study combined 103 newly assembled pea plastomes with 42 previously published plastomes to construct the first pea pan-plastome. The lengths of plastomes varied from 120,826 to 122,547 bp, with an average GC content of 34.8%. Protein-coding genes in the pan-plastome exhibited a strong bias towards A/T in the third codon position, with a notably high frequency of the amino acid arginine (RSCU value = 4.8) among plastome-encoded proteins. Additionally, the codon usage of petB, psbA, rpl16, rps14, and rps18 showed extreme influence from natural selection. Moreover, the genes ycf1, rpoC2, and matK were identified as hypervariable regions, suggesting their potential utility as DNA barcoding loci to distinguish maternal lineages for breeding and other agronomic purpose. The phylogenetic results indicated that cultivated peas had undergone at least two independent domestications, originating from the PA and PS groups. Compared to former research based on nuclear data, the PSeI-a group and PSeI-b group were newly found branched between the PA group and PF group.