At the age of 22 he married his wife, Nicole, with whom he has had two daughters.
While working at the museum he, along with his colleague Jean Dorst, who later replaced Berlioz as the head of the ornithology department, helped write the species description for the Djibouti francolin, a critically endangered francolin endemic to Djibouti whose type specimen was brought to the museum.
He also developed a lifelong interest in two distinctly different bird families, the hummingbirds and the petrels.
In 1955 Jouanin published his first independent species description after realizing that the new species, named Jouanin's petrel, differed significantly from the Mascarene petrel.
This description began a long period of his life dedicated to the research of petrels in the Indian Ocean.
He then proceeded to study Cory's shearwater in the Madeiras with Alec Zino, a collaboration that has resulted in over eighty publications.Jouanin is recognized as an expert on the Order Procellariiformes and co-wrote the section on those birds in James Lee Peters's Check-list of Birds of the World.