In this study, we used the next-generation sequencing method to obtain mitochondrial DNA (mtDNA) of Porzana paykullii, Rallus aquaticus and Gallirallus striatus in Gruiformes, and Hydrophasianus chirurgus in Charadriiformes, after which we analysed and compared structure, phylogeny, and taxonomic origin of the Gruiformes and Charadriiformes. Based on sequencing, splicing, and annotating the mtDNA of four birds, the results showed that the lengths of mtDNA were 16,955 bp in Porzana paykullii, 17,149 bp in Rallus aquaticus, 17,647 bp in Gallirallus striatus and 16,855 bp in Hydrophasianus chirurgus, respectively. The base compositions were A > C > T > G in 73 species complete mitochondrial sequences in Gruiformes and Charadriiformes. The total AT content in the 73 species was larger than that of GC. The start codons in protein-coding genes (PCGs) included ATG, GTG, ATT, ATC and ATA, while its stop codons included TAA, TAG, AGG, AGA and the incomplete cipher T. In PCGs, the highest frequency of codon was CTA (Leu). The highest frequency of amino acids was Leu, whereas the lowest was Cys. In phylogenetic analyses, Gruiformes included Grui and Ralli, and Charadriformes included Charadrii, Lari and Scolopaci. The genus Porzana was closest to Porphyrio. Gallirallus striatus and Lewinia muelleri consisted a sister group, while Rallus aquaticus was a separate branch. Hydrophasianus chirurgus (Charadriiformes: Jacanidae) was closely related to Rostratulidae. According to the estimation of divergence time corrected by fossil records of related birds and compared with previous studies, the base divergence time of Gruiformes was 46.33 (58.46~25.60) Ma, the emergence time of the suborders Grui was about 17.62 (29.76~4.15) Ma, and the emergence time of the suborders of the Ralli was about 32.18 (46.17~19.69) Ma. The origin time of Charadriiformes was about 45.44 (58.21~24.67) Ma. The origin time of the Charadrii was 44.52 Ma (52.66 ~ 23.55 Ma). The divergence time of Charadrii, Lari and Scolopaci was about 33.46 (43.44~22.92) Ma, 29.10 (40.67~16.43) Ma and 27.06 (34.83 ~ 12.72) Ma, respectively.