One of the major technological advances in biological research was the invention and development of the transmission electron microscope, which enables high resolution and high magnification studies of cross-sections of specimens. As such, it has proved to be a useful tool to describe ultrastructural features of taxonomic and phylogenetic importance in modern organisms. Here we discuss how to extend the use of transmission electron microscopy (TEM) to the fossil record, with emphasis on acritarchs (organic-walled microfossils of unknown affinity). Microfossils are traditionally studied by use of transmitted light microscopy, a method that reveals details of external morphology only. TEM however, gives an additional level of detail and reveals structures that can greatly aid in interpretation of taxonomic affinity, and thus can reveal further detail on the origination and diversification of myriad eukaryotic groups in the fossil record. In this chapter we describe the preparation procedure, show advantages and shortcomings of the technique, and discuss how to interpret the results from a geobiological perspective.