Jonathan Paul Auer (born September 29, 1969) is an American musician who co-founded the power pop band The Posies, along with Ken Stringfellow. Auer and Stringfellow also participated in the rejuvenated Big Star and in 2003 released Private Sides, a six-song split EP (Arena Rock Recording Co./Rykodisc). Auer played guitar on the 2004 William Shatner record Has Been which was produced and arranged by Ben Folds.

Auer was a founding member of Sky Cries Mary, a member of The Squirrels, Lucky Me, Jean Jacket Shotgun and Chariot. As a solo artist, his credentials include: an EP, 61/2 and a full-length record on the label Pattern25 called Songs from the Year of Our Demise. As a record producer, he has worked with bands such as You Am I, Monostereo, Cheap Star, Love Battery, Redd Kross, Truly, The Melismatics, and Tad.