Abstract Nine non-pollen palynomorph (NPP) groups occur in Quaternary marine and brackish-water sediments; these groups represent various planktonic or micro- to macrobenthic organisms. Some extant NPP were previously classified as fossil Acritarcha, Chitinozoa or scolecodonts. We refer to reviews of these fossils and their applications for Paleozoic–Mesozoic biostratigraphy and palaeoecology but focus on extant marine NPP that can be studied by laboratory culture, genetics or micro-geochemical methods. Marine NPP include resting cysts of planktonic dinoflagellates and prasinophytes, tintinnids and other cilates, copepod eggs and skeletal remains, and various microzoobenthos: microforaminiferal organic linings, ostracod mandibles and carapace linings, various worm egg capsules and mouthparts. New micro-Fourier Transform Infrared spectroscopy spectra suggest the probable affinities of the tintinnid cyst type P and Beringiella . Our applications in marine biodiversity and provincialism studies emphasize under-studied polar regions and neglected ice-algae nano-plankton and compare climate-based NPP distributions to Ocean Biogeographic Information System realms. Trophic relationships are outlined using sediment-trap studies. Seasonal to annual-scale investigations of palaeoproduction provide new perspectives on ocean carbon budgets during times of rapid climate change and atmospheric carbon increase. More taxonomic and source-linkage studies of non-dinocyst marine NPP are needed but we outline potentials for studies of hemispheric or global-scale shifts in marine food webs as driven by ocean warming.