Approximately one-third of the c. 1200 polycystine radiolarian names currently recognized as valid in deep-sea research (Cenozoic sediments and plankton) come from the first century of taxonomic studies (c. 1840–1930). German scientists dominated early research on radiolarian biology and taxonomy. C. G. Ehrenberg’s initial work was followed by E. Haeckel’s mammoth monographic works, particularly his Challenger report. Other important early workers were D. Rüst on Mesozoic and Palaeozoic forms and A. Popofsky on plankton and sediment materials, with smaller contributions by J. Müller, E. Stöhr, F. Dreyer and H. Mast. Excluding Haeckel, these workers together published over 2000 species names. A fraction (5–25%) of these names are still used today in deep-sea research, with a tendency for more prolific authors to have higher modern usage rates. Haeckel’s legacy is different. He published over 5000 species names, but only a few percent are still used. The reasons for his species names no longer being used seem to include both factors common to disuse of names from other early authors (inadequate text descriptions, poor or absent illustration, no preserved original materials) but also due to substantial duplication of species and genus names, created by imposition of a partially artificial high level taxonomy. Based on Haeckel’s own writings and by analogy to other parts of Haeckel’s work, it is suggested that Haeckel’s desire to discover and show evolutionary relationships lay behind this flawed approach to taxonomy.