He began to see the advantages of opening up the Mekong River to French colonisation. He had support from the Marquis de Chasseloup-Laubat, Minister of the Marine and Colonies and Admiral Pierre-Paul de La Grandière, commander of the Cochinchina naval station. The latter thought him too young and inexperienced to take command of such an expedition so it was given to Captain Doudart de Lagrée (1823-68).
Leaving Saigon on 5 June 1866 they discovered the 20 metre-high Khone Falls on 18 August. Any thought of using the river for trade disappeared. The expedition split into two different parties, one exploring to the east and one to the west (including Angkor Wat). After several months they met and headed northwards, reaching Vientiane on 4 April 1867. They reached Luang Prabang, the capital of Laos, on 29 April. At several points Lagrée wanted to abandon the expedition due to political uncertainty in the region, but Garnier insisted. They continued further upriver, before crossing overland from the Mekong River to search for the Red River. They reached Yuan-chiang on the river on 17 November. Wanting to return down the Red River, Lagrée was again convinced by Garnier and they continued to the north entering China and arriving at Kunming on 23 December.
At the suggestion of French missionaries, the expedition continued north to Huitse, where Lagrée fell ill. Garnier led the expedition henceforth and decided to leaving Lagrée there to recover. A detachment went to Talifu, the capital of Sultan Suleiman, leader of the Yunnan rebels. Upon his return Garnier learnt that Lagrée had died. Exhuming his body, Garnier travelled down the Yangtze River to the Chinese coast, and via Shanghai went back to Saigon where Lagrée was buried.
The expedition covered over 6000 kilometres of previously undiscovered terrain. It mapped the course of the Mekong River as far as Keng Hung. Despite finding that it was not a viable trading route to the interior the Red River was considered a good prospect. Henceforth French efforts concentrated on extending colonial rule northwards from Cochin China. The maps in this work are after Garnier, whilst the magnificent series of views are taken from sketches by the expedition artist Louis Delaporte (1842-1925). These include fine depiction’s of the ancient capital of Laos at Viet Chan and Angkor in Cambodia. Cordier Sinica 329; Cordier Indosinica 1012; Howgego 1850-1940 Continental Exploration G4 (omitting atlas volume). Howgego 1850-1940 Continental Exploration G4 (omitting atlas volume).
Voyage d'Exploration en Indo-Chine effectue pendant les annees 1866, 1867, et 1868 par une commission Francaise Presidee par M. Le Capitaine de Fregate Doudart de Lagree