This city is located between Nogales and Hermosillo, the State Capital.

Magdalena´s actually territory was originally occupied by natives: Pápagos and Pimas Altos.

When missionary Father Euebio Francisco Kino arrived in 1687, he found a small ranch called Buquivaba (house beside water) near Magdalena River inhabited by Pima Indians. In there, he established the Mission Santa María de Magdalena de Buquivaba. This mission was destroyed by Father Kino himself. Father Eusebio Kino died at Magdalena Mission on March 15, 1711, place where his remains rest.

Magdalena used to be part of the district in the second half of the XIX century. On October 1st, 1923 it received the title as city. In 1966 it obtained the name of Magdalena de Kino.