Flacourt restored order among the French soldiers, who had mutinied, but in his dealings with the natives he was less successful, and their intrigues and attacks kept him in continual harassment during his entire term of office.
In 1655 he returned to France. Not long after he was appointed director general of the company; but having again returned to Madagascar, he drowned on his voyage home on the 10th of June 1660. He is the author of a Histoire de la grande isle de Madagascar (1st edition 1658, 2nd edition 1661).
Flacourt was one of the few, if not the only, Western person(s) to have recorded knowledge of the elephant birds of Madagascar when they were possibly still extant. Flacourtia, a genus of flowering plants in the willow family, Salicaceae, was named in honor of him. See A. Malotet, Ét. de Flacourt, ou les origines de la colonisation française à Madagascar (1648–1661), (Paris, 1898).
- Everett, Thomas H. (1981). The New York Botanical Garden Illustrated Encyclopedia of Horticulture. 4. Courier Corporation. p. 2376. ISBN 978-0-8240-7234-6.
- This article incorporates text from a publication now in the public domain: Chisholm, Hugh, ed. (1911). . Encyclopædia Britannica. 10 (11th ed.). Cambridge University Press. p. 454.
- Kay, J. (2004). "Étienne de Flacourt, L'Histoire de le Grand Île de Madagascar (1658)". Curtis's Botanical Magazine. 21 (4): 251–257. doi:10.1111/j.1355-4905.2004.00448.x.
- Histoire de la Grande Isle Madagascar – online book (French)