The large organ of Santa María Tamazulapan was an impressive instrument in both appearance and sound. It was the first Oaxaca-built instrument with an extended keyboard of 54 notes. This innovation was already evident in earlier organs in the state built by Puebla organ builders, but it wasn´t adopted locally until this construction in 1840. The organ builder, José Domingo Martínez Bonavides, was related to the Martinez dynasty of organists and organ builders and alternated as the first or second organist in the Oaxaca Cathedral (ca.1800-1823). The organ is situated in a tribune on the left side of the church and faces a small restored table organ across the nave. Typical of the era, it is unpainted but exhibits fine neo-classical decorative carvings, including pipeshades in the form of butterflies as in the later Tlaxiaco organ. Unfortunately, a local blacksmith removed all its pipes except for the five largest in the 1950s to use as raw material. 

Documentation confirms the proposed construction of a monumental organ in 1776 which would have been the largest organ ever in Oaxaca (9.5 m high, 5 m wide). However, the organ builder died while the work was in process, and the organ was never finished. This instrument would have filled the tribune occupied by the current unrestored organ. Vestiges of the impact this huge instrument would have had on the architecture of the left side of the Tamazulapan church are still visible today. (See History)