Balete grew up in the Bicol Region of Luzon. From 1984 to 1988 he studied at the University of the Philippines in Los Baños , where he obtained the Bachelor of Science in Zoology. In 1989 he became a member of the Philippine Mammal Project of the Field Museum of Natural History. He spent eight months of the year as an expedition leader in the rainforest and about four months with a research team from the Field Museum of Natural History.
In 2000, Balete began a 15-year long-term study of the mammals of the island of Luzon. The project team, made up of Filipino and US scientists, included Balete, Lawrence R. Heaney of the Field Museum of Natural History, Mariano Roy Duya and Melizar Duya of the University of the Philippines, Sharon Jansa of the University of Minnesota, Eric Rickart of the Natural History Museum of Utah and Scott Steppan of Florida State University . Of 56 non-flying mammal species, 52 are endemic to Luzon and 28 mammal species were rediscovered during this study. Also 57 species of bats occur on Luzon. In 2008 Balete and Heaney on Pulagon Luzon made the rediscovery of the Blacktail Luzon Tree Rat ( Carpomys melanurus), a rodent that had been considered lost for 112 years. In 2016, he published with Lawrence R. Heaney and Eric A. Rickart a book on the mammals of Luzon entitled The Mammals of Luzon Island: Biogeography and Natural History of a Philippine Fauna.
Balete is a member of the Haribon Foundation, the largest conservation organization in the Philippines.
Besides several rodent species, including Archboldomys musseri, Crunomys suncoides, Apomys aurorae, Apomys banahao, Apomys brownorum, Apomys iridensis,  Apomys magnus, Apomys minganensis, Apomys lubangensis, Apomys sierrae, Apomys zambalensis, Batomys uragon, Rhynchomys banahao, Rhynchomys isarogensis, Rhynchomys labo and Rhynchomys mingan, Balete described the four lizard species Brachymeles lukbani, Parvoscincus boyingi, Parvoscincus hadros and Parvoscincus igorotorum. Balete's research also focuses on indigenous members of the Rafflesia plant genus.
In 2006, Julie F. Barcelona, Mary Ann O. Cajano and Annalee S. Hadsall described the Rafflesia species Rafflesia baletei, which was discovered in 1991 by Balete on the Isarog volcano in the Bicol Region.
- Deutsche Welle: Cloud rats of the sky islands: 28 new mammal species found in the Philippines (19 July 2016). Accessed 16 November 2016
- Heaney, Lawrence Richard; Balete, Danilo S.; Duya, Mariano Roy M.; Duya, Melizar V.; Jansa, Sharon A.; Steppan, Scott J.; Rickart, Eric A. (2016). "Doubling diversity: a cautionary tale of previously unsuspected mammalian diversity on a tropical oceanic island" (PDF). Frontiers of Biogeography. 8 (2). doi:10.21425/F5FBG29667. ISSN 1948-6596. pdf
- LiveScience: Cloud Rat Rediscovered after 112 Years
- Rickart, EA, Heaney, LR, Balete, DS & Tabaranza, Jr., BR (1998) A review of the genera Crunomys and Archboldomys (Rodentia, Muridae, Murinae) with descriptions of two new species from the Philippines. Fieldiana Zoology new series, 89, 1-24.
- Heaney, L.R.; Balete, D.S.; Rickart, E.A.; Alviola, P.A.; Duya, M.R. M.; Duya, M.V.; Veluz, M.J.; VandeVrede, L.; Steppan, Scott J. (2011). "Chapter 1: Seven New Species and a New Subgenus of Forest Mice (Rodentia: Muridae: Apomys) from Luzon Island". Fieldiana Life and Earth Sciences. 2: 1–60. doi:10.3158/2158-5520-2.1.1. ISSN 2158-5520. pdf
- Heaney, Lawrence R.; Balete, Danilo S.; Veluz, Maria Josefa; Steppan, Scott J.; Esselstyn, Jacob A.; Pfeiffer, Andrew W.; Rickart, Eric A. (2014). "Two new species of Philippine forest mice (Apomys, Muridae, Rodentia) from Lubang and Luzon Islands, with a redescription ofApomys sacobianusJohnson, 1962". Proceedings of the Biological Society of Washington. 126 (4): 395–413. doi:10.2988/0006-324X-126.4.395. ISSN��0006-324X. pdf
- Balete, D.S.; Rickart, E.A.; Heaney, L.R.; Jansa, S.A. (2015). "A new species ofBatomys(Muridae, Rodentia) from southern Luzon Island, Philippines". Proceedings of the Biological Society of Washington. 128 (1): 22–39. doi:10.2988/0006-324X-128.1.22. ISSN 0006-324X. pdf
- Balete, Danilo S.; Rickart, Eric A.; Rosell-Ambal, Ruth Grace B.; Jansa, Sharon; Heaney, Lawrence R. (2007). "Descriptions of two New Species of Rhynchomys Thomas (Rodentia: Muridae: Murinae) from Luzon Island, Philippines". Journal of Mammalogy. 88 (2): 287–301. doi:10.1644/06-MAMM-A-090R.1. ISSN 0022-2372.
- Rickart, E.A.; Balete, D.S.; Timm, R.M.; Alviola, P.A.; Esselstyn, J.A.; Heaney, L.R. (2019). "Two new species of shrew-rats (Rhynchomys: Muridae: Rodentia) from Luzon Island, Philippines". Journal of Mammalogy. doi:10.1093/jmammal/gyz066. ISSN 0022-2372.
- Siler, C.D.; Balete, D.S.; Diesmos, A.C.; Brown, R.M. (2010). "A New Legless Loam-swimming Lizard (Reptilia: Squamata: Scincidae: Genus Brachymeles) from the Bicol Peninsula, Luzon Island, Philippines". Copeia. 2010 (1): 114–122. doi:10.1643/CH-08-231. ISSN 0045-8511.
- Brown, R.M. et al. (2010) "Species boundaries in Philippine montane forest skinks (Genus sphenomorphus): three new species from the mountains of Luzon and clarification of the poorly known S. beyeri, S. knollmanae, and S. laterimaculatus." Scientific Papers Natural History Museum The University of Kansas (42): 1-27
- Barcelona, J.F., Cajano, M.A.O. & Hadsall, A.S. (2006) Rafflesia baletei, Another New Rafflesia (Rafflesiaceae) from the Philippines. Kew Bulletin 61(2): 231-237 pdf
- IPNI. Balete.
- International Plant Name Index: Author: Danilo S. Balete
- Profile: Danilo S. Balete at LinkedIn
- Profile: Danilo S. Balete at the Field Museum of Natural History