Gundlach graduated from Marburg University, where his father was professor of physics, as Doctor of Philosophy in 1837. In 1839, he left Europe to make collections on the Caribbean island of Cuba, where he lived ever since. During a short trip to Puerto Rico, at the request of Jesuit fathers to offer assistance in the creation of a zoological collection, in 1868, when revolutionary activities were beginning in Cuba as well as Puerto Rico, he met with don Tomás Blanco, according to naturalist Dr. Agustin Stahl. A friend of Carl Wilhelm Leopold Krug, who served as German Vice Consul in Mayagüez, Puerto Rico and who paid for some of Gundlach's travels, he visited Puerto Rico in 1873, leaving Havana on 4 June 1873 on the ship Manuela, arriving in Mayagüez, Puerto Rico on 13 June, staying in Puerto Rico for approximately six months. During that trip, Gundlach contributed to the founding of the Civil Institute for Secondary Learning or "Instituto Civil de Segunda Enseñanza". This institute was closed several months later, in keeping with the Spanish government's policy, expressed to the bishops of Santiago in Cuba and of San Juan, of limiting the opportunities for higher learning, both in Cuba as well as Puerto Rico. He subsequently travelled from Havana to Puerto Rico's west coast aboard the "Marsella" in September 1875. He remained in Puerto Rico for approximately one year during that trip. While he was there, he changed his name from Johannes Christoph to its Spanish equivalent Juan Cristóbal. He wrote the first major work on the birds of Cuba, Ornitología Cubana, and his name is recorded in the scientific names of over sixty species. His collections passed into the care of the Museo Poey in Havana, named after Cuban intellectual Dr. Felipe Poey y Aloy (1799–1891), upon his death in 1896.
His visits to Puerto Rico were considered so important to the development of the study of natural sciences in Puerto Rico that he is considered "the Father of Natural Sciences in Puerto Rico" and his portrait, painted by Andrés Garcés, hangs in the School of Natural Sciences at the University of Puerto Rico Río Piedras campus. To honor him, Dr. Agustín Stahl named a species of the cupey tree in his honor as Clusia gundlachi. The Puerto Rico Academy of Arts and Sciences on June 26, 2008, awarded recognitions that carry Gundlach's name to 25 prominent scientists in Puerto Rico.
He wrote Contribucion á la Erpetologia Cubana (1880) and Contribucion á la entomologia Cubana in 4 volumes (1881–1884).
Species named for Gundlach
- Accipiter gundlachii – Gundlach's hawk
- Bufo gundlachii – Gundlach's Caribbean toad
- Cazierus gundlachii – a Cuban scorpion
- Dendroica petechia gundlachi – subspecies of yellow warbler (petechia group)
- Palinurellus gundlachi – Caribbean furry lobster
- Vireo gundlachii – Cuban vireo
- Gundlachia – a genus of land snails
- Gundlachia – a genus of plants
- Nephronaias gundlachii – another land snail
- Anolis gundlachi – a lizard living in Puerto Rico
- Anolis juangundlachi – a lizard living in Cuba
- Clusia gundlachi – a vine endemic to Puerto Rico
- Unio gundlachi – a freshwater bivalve
- Strumigenys gundlachi – a Neotropical dacetine ant
- Camponotus gundlachi – a Cuban carpenter ant
- Temnothorax gundlachi – a Cuban ant
- Acmaeodera gundlachi – a buprestid beetle
- Neolema gundlachiana – a leaf beetle
- Lasioglossum (Dialictus) gundlachii – a halictid bee
- Works by or about Juan Gundlach at Internet Archive
- Wilhelm Hess (1904), "Gundlach, Johannes", Allgemeine Deutsche Biographie (ADB) (in German) 49, Leipzig: Duncker & Humblot, pp. 634–635
- Plants named for Gundlach at IPNI
- "Gundlach, Juan". Appletons' Cyclopædia of American Biography. 1892.
- Vilaro, Juan, Sketch of John Gundlach, Popular Science vol 50, no 42, March 1897 (Google Books)