The Marine Mammal Center says only about 60 of these porpoises exist and that less than half are females that can reproduce.
Vaquitas live in the waters of the northern Gulf of California in Mexico.
But so does a type of fish that's illegally trafficked to Asia, where its swim bladder is in high demand. Poachers use nets to catch the fish, and oftentimes vaquitas are caught right along with them.
To help the porpoises, the Navy is training its dolphins to seek out the remaining vaquitas and relocate them to a protected area.
The operation is a joint one with Mexico's Ministry of Environment and Natural Resources.
"Undoubtedly this is going to be the last call that the vaquita has, and as President Peña Nieto instructed us, we will make every effort we can to prevent its extinction," Rafael Pacchiano, Mexico's secretary of environment and natural resources, told a local paper in December.
However, since vaquitas have never been held in captivity, the director of World Wildlife Fund Mexico is worried the porpoises will end up dying anyway.
The U.S. Navy most often trains its dolphins to use their sonar to detect intruders and underwater mines, as well as find lost equipment in murky water or at deep depths.
The vaquita operation is set to begin in May.