A guide for the sampling and analysis of mixoplankton in natural environments is provided that offers guidelines to assist students and research scientists initiating studies of mixoplankton in natural waters. The guide contains methods on how to sample, preserve and analyse mixoplankton abundance and diversity directly from natural environments. As mixoplankton are fully integrated constituents of the protist plankton community, many of the sampling strategies and techniques described in this guide are applicable also to phytoplankton and protozooplankton. Accordingly, methods cover traditional methods but also evolving new molecular techniques developed for applications to field and discrete studies of plankton diversity.