The organ at the Penn Yan First Baptist Church has a heritage which dates back to 1871.

At the time of the construction of the present church building, William A. Johnson of Westfield, Massachusetts was selected to furnish the church with a new pipe organ. Johnson had been building organs for 28 years, and had earned a reputation as a builder of fine quality instruments, both musically and mechanically. (See this Wikipedia article.)

The organ, Johnson's opus 345, was originally installed in the archway at the rear of the sanctuary. It was a two manual "tracker" (mechanical action) organ containing around 1,000 pipes in about 18 ranks. An 1871 news article stated "And to make the church even more attractive, a large and very melodious organ has been added, at a cost of $2,100, which gives entire satisfaction, and has been pronounced by competent judges a fine instrument."

In 1904, as a part of a major remodeling of the sanctuary, the organ was moved from the rear to the front arch. It may have been at this time that a "water motor" was added to pump the organ's bellows. Before that, the wind supply was provided by man power - or often boy power - by the operation of a long lever attached to the bellows. No other changes in the organ have been found in church records until 1931.

In 1931, a "new" organ was built by the Marr and Colton firm of Warsaw, NY. However, it was not completely new, as the majority of it's pipework came from the 1871 instrument. The tracker (mechanical) action was replaced by electro-pneumatic action chests, and a new console was provided. The entire structure of the organ was changed by the removal of the 1871 casework and the installation of the pipework in three chambers across the front of the sanctuary.

The present instrument contains around 1200 pipes. It's character is more Johnson than it is Marr & Colton, a theater organ company which had moved into church organ construction with the advent of the "talkies". Since a big share of the pipework is from the 1871 organ, it's quality of tone retains much of the character of the highly respected organs built by Wm. A. Johnson.