Fungi in marine ecosystems play crucial roles as saprotrophs, parasites, and pathogens. The definition of marine fungi has evolved over the past century. Currently, “marine fungi” are defined as any fungi recovered repeatedly from marine habitats that are able to grow and/or sporulate in marine environments, form symbiotic relationships with other marine organisms, adapt and evolve at the genetic level, or are active metabolically in marine environments. While there are a number of recent reviews synthesizing our knowledge derived from over a century of research on marine fungi, this review article focuses on the state of knowledge on planktonic marine fungi from the coastal and open ocean, defined as fungi that are in suspension or attached to particles, substrates or in association with hosts in the pelagic zone of the ocean, and their roles in remineralization of organic matter and major biogeochemical cycles. This review differs from previous ones by focusing on biogeochemical impacts of planktonic marine fungi and methodological considerations for investigating their diversity and ecological functions. Importantly, we point out gaps in our knowledge and the potential methodological biases that might have contributed to these gaps. Finally, we highlight recommendations that will facilitate future studies of marine fungi. This article first provides a brief overview of the diversity of planktonic marine fungi, followed by a discussion of the biogeochemical impacts of planktonic marine fungi, and a wide range of methods that can be used to study marine fungi.