1989

• Hoeksema B.W., 1989. Taxonomy, phylogeny and biogeography of mushroom corals (Scleractinia: Fungiidae). Zoologische Verhandelingen, Leiden 254: 1-295., available online at https://web.archive.org/web/20150924090552/http://www.repository.naturalis.nl/document/149013 .

2003

• Achituv, Y. & Hoeksema, B.W. 2003. Cantellius cardenae spec. nov. (Cirripedia: Pyrgomatinae) from Acropora (Isopora) brueggemanni (Brook, 1893) (Anthozoa:Acroporidae), a case of host specificity in a generalist genus. Zoologische mededelingen, 77(1): 1–8. Full article (PDF)Reference page. 

2015

• Van Soest, R.W.M., Hoeksema, B.W., Reimer, J.D. & De Voogd, N.J. 2015. New records of the rare calcareous sponge Paragrantia waguensis Hôzawa, 1940. ZooKeys 546: 1–20. DOI: 10.3897/zookeys.546.6122 Reference page. 

• Waheed, Z., Benzoni, F., van der Meij, S.E.T., Terraneo, T.I. & Hoeksema, B.W. 2015. Scleractinian corals (Fungiidae, Agariciidae and Euphylliidae) of Pulau Layang-Layang, Spratly Islands, with a note on Pavona maldivensis (Gardiner, 1905). Zookeys 517: 1-37. DOI: 10.3897/zookeys.517.9308 Full article Reference page. 

2016

• Meyers-Muñoz, M.A., van der Velde, G., van der Meij, S.E.T., Stoffels, B.E.M.W., van Alen, T., Tuti, Y. & Hoeksema, B.W.W. 2016. The phylogenetic position of a new species of Plakobranchus from West Papua, Indonesia (Mollusca, Opisthobranchia, Sacoglossa). ZooKeys 594: 73–98. DOI: 10.3897/zookeys.594.5954 . Reference page. 

• Stoffels, B.E.M.W., van der Meij, S.E.T., Hoeksema, B.W., van Alphen, J., van Alen, T., Meyers-Muñoz, M.A., de Voogd, N.J., Tuti, Y. & van de Velde, G. 2016. Phylogenetic relationships within the Phyllidiidae (Opisthobranchia, Nudibranchia). ZooKeys 605: 1-35. DOI: 10.3897/zookeys.605.7136 . Reference page.