Martin Rosales Magana had been on the run, persecuted by rival gang the Knights Templar.
Officials say Rosales Magana was trying to forge an alliance with another cartel, The Zetas, to launch a mass attack on the Knights Templar with more than 200 gunmen.
The pseudo-religious La Familia has been decimated by arrests and killings, and displaced by the Knights Templar from its home state of Michoacan.
Rosales Magana had been on the run since Knights Templar threatened to kill relatives of those who still sympathized with La Familia, according to Mexican federal police.
Rosales Magana and three other men were arrested Tuesday in the neighboring State of Mexico.
The Associated Press contributed to this report.