The organ of San Pedro Mártir Yucuxaco is one of Oaxaca’s least altered historic instruments and one of the most appreciated by organ experts. The date of construction, 1740, and a Maltese cross are etched on the central façade pipe and in the back interior of the case. Another cross appears on the first pallet of the wind chest. The case was built of good hard wood and has not been damaged by woodworm. However, its general aspect is austere, and only the pipeshades have decorative carvings. Incorporated into the carvings of the central tower are two faces with indigenous features in profile in mirror image. This detail is unique, but its significance may never be known. The organ’s disposition is identical to that of Zautla, and of Quiatoni and Tlacochahuaya before their modifications. The bass and treble registers are similarly not parallel and are reinforced in different ways.  The left hand follows a standard progression, whereas the right hand doubles the 4´ flautado and 2´ octava pitches. The interiors of these three organs may have been similar, but their exteriors were not because Yucuxaco was not painted with religious imagery. A small paper with a Dominican cross finely drawn in black ink is the only decoration on the front of the case.

The organ retains nearly all its original pipes and mechanical components. A paper label inside the case cites a repair in 1840 by Joaquin Bonavidiz (Bonavides) of the Martinez dynasty of organ builders. At that time or during a later intervention, new stop labels were added above the lateral slider tabs. They are more or less intact and legible on the left side, but were removed on the right. The keyboard is original and is in surprisingly good condition after nearly three centuries. Perhaps the organ was not played regularly. Stickers identifying the keys C, D, E, etc. (not the solfege system) were added to the keyboard, probably because teaching material used that system. The organ was originally located on the church floor, then moved up to the new choir loft in the 1940s. It was moved back down while the wooden roof of the church was rebuilt of brick in 1975. It was again moved back up, but it is unknown if the organ survived so much movement and was still functioning by then. If not, the bellows and its table, which had been originally located in the niche behind the organ, might have disappeared.  The missing front panel of the case was replaced by the IOHIO in 2022.