Restoration: 1996-98, organ restored by Pascal Quoirin; case and façade pipes restored by Babou Quoirin. Project directors Gustavo Delgado and Ofelia Gómez of the Academia Mexicana de Música Antigua para Órgano (AMMAO); financed by Fomento Cultural Banamex.

The magnificent organ of Santo Domingo Yanhuitlán is situated in a high tribune on the left side of the immense choir loft. It resounds in one of the most dramatic spaces, both acoustically and aesthetically, in the American continent. The church and monastery complex served as the Dominican base in the Mixteca Alta, and the friars had direct access to the choir loft to play the organ. The Dominican friar Francisco de Burgoa in 1674 refers to a second smaller organ below in the church for the less important celebrations. The fanciful painted decoration on the lower case resembles that of the Basílica de La Soledad and may have been painted by the same artist. Because of the similarities, it's possible that the Yanhuitlán organ was built around the same time as the 1719 Soledad organ. Here we see stylized birds in profile instead of the fanciful human forms in La Soledad which similarly merge into swirling volutes. The upper case is richly carved and gilded. Rows of oval medallions, a typical baroque feature also seen on altarpieces and church façades, adorn the façade of the organ. Several contain Dominican symbols (the only such organ in Oaxaca): the black and white cross, the eight-pointed star, and the dog bearing a torch while playing with the world globe. A serene statue of Saint John the Baptist, perhaps not original, stands on top of the central tower. Hidden deep within the carvings at its base is the agonized face of a Moor being crushed by the weight of the enormous organ pipes, as a symbol of the power of the Catholic church. These are the only façade pipes on a monumental organ that retain their original ferocious faces and floral designs. The other similar organs in Oaxaca City were not so lucky. The pipe painting was scraped off in the Cathedral and painted over with enamel in La Soledad. The background color of the case is rusty brown and may have been green originally like its counterparts. However, it may have changed over time because of a chemical reaction of the paint.

The organ builder Jesús Cano made extensive modifications to the organ in 1886-1887. He built a new keyboard adding C and D to the bass, but not C# and D#, thus only partially eliminating the short octave. He rebuilt the windchest and roller board, replaced damaged pipes, removed the horizontal reed pipes (clarín), and built a reserve bellows to replace the original three wedge bellows (the frames still exist). It seems that Jesús and his relatives had a shop in the nearby town of Chachoapam and worked extensively in the Mixteca Alta during the 1870s and 1880s. During the 1998 restoration, the organ builder Pascal Quoirin reconstructed the clarín and other missing or damaged pipes. A new small wedge bellows was placed next to the motor. However, since there is only one, the winding system can’t be operated manually. The organ is unfortunately played rarely, but it is most appreciated.