The Batavia Muckdogs are a collegiate summer baseball team in the Perfect Game Collegiate Baseball League (PGCBL). They are located in Batavia, a city in Genesee County, New York, United States. Their home field is Dwyer Stadium in the city of Batavia, built after the 1996 season to replace the original Dwyer Stadium (formerly State Street Park, MacArthur Stadium) that opened July 27, 1938 as home to the Batavia Bees, a semi-pro team in the Genesee County League.

Off and on from 1939 to 2020, they were members of Minor League Baseball's New York–Penn League (NYPL). With Major League Baseball's reorganization of the minor leagues after the 2020 season, Batavia and the New York-Penn League were eliminated from affiliated baseball. The Muckdogs later joined PGCBL for the 2021 season. Their 2022 season and the loss of professional baseball in Batavia was chronicled by author Will Bardenwerper in "Homestand: Small Town Baseball and the Fight for the Soul of America."

Prior to the current Batavia franchise, professional baseball in the city dates back to 1897 when Batavia played in the New York State League. The Batavia Giants, sometimes referred to as the Reds because of their crimsons uniforms, were the first classified team in the city making their debut - after some rainouts - on May 14, 1897, against the Auburn franchise at a stadium built on Swan Street; future major leaguer Jack Burns batted third and played shortstop. After a rough start to the season, where the team lost their first 9 games, the team released eight players and fired manager Martin Earley. J.J. Benner took over the club as team captain and acting manager, however play did not improve and he was replaced by former major leaguer Joe Hornung who was named player-manager on May 24, he made his debut in the lineup on June 14 at 40 years old, going hitless. After 20 games the team sat at 4–16 and had money troubles where local fans would not pay the 10 cent admission, Hornung left the team on July 9. It was announced on July 24 that the team would move to Geneva, by July 25 the team had left Batavia and become the Geneva Alhambras. That season the Class-C New York State League also consisted of teams in Canandaigua, Cortland, Lyons, Palmyra, and Auburn.

As was popular across the country, Batavia hosted many semi-pro leagues prior too, and after, the Giants left town. This included the Western New York League along with teams in nearby Le Roy, Perry and Warsaw. The Batavia Bees were the popular semi-pro team prior to professional baseball coming back to Batavia in 1939, and they continued play even after the Clippers arrived.

The history of the New York–Penn League originated in Batavia as the league, then known as the Pennsylvania–Ontario–New York League (PONY League), was formed in a local hotel that has since been demolished. Original league cities included Batavia, Bradford, Hamilton, Jamestown, Niagara Falls, and Olean.

The Muckdogs were founded in 1939 as the Batavia Clippers, however the team was not in operation during the 1954–56 and 1960 seasons after dropping out of the league for financial reasons. During the 1957 through 1959 seasons the team was known as the Batavia Indians, upon their final return to the league in 1961 the team was known as the Batavia Pirates until changing their name to the Batavia Trojans in 1966 until 1987.

From 1988 through the 1997 season the team brought back the historic Batavia Clippers name before changing to the Muckdogs in 1998 based on a fan poll that chose the nickname and logo. The "Muckdogs" name was inspired by Genesee County's mucklands. Batavia celebrated their 80th anniversary during the 2019 seasons as the only founding member of the league still in existence.^{[citation needed]}

The Muckdogs franchise was surrendered to the league prior to the 2018 season. The team was then operated as a ward of the league.