The present study was designed to gain insight into the protists and fungi that made up the microbiota in the past, fossilized in two different substrates: amber and sandstone. The amber, dated as Lower Cretaceous, was from Álava in northern Spain, while fossil-bearing sandstone rocks were collected from the Linnaeus terrace and Mount Fleming regions of Antarctica. When examining this type of inclusion in hard substrates, it first has to be established whether the microorganism is mummified or only partially mineralized. In the latter case, some of the organism’s autofluorescence may be preserved. In our amber samples, light microscopy revealed a very well preserved microcenosis in what must have been a semiaquatic habitat comprised of several types of protozoa including Amoeba, Paramecium and Astasia (Euglena), Amebas limax and the colpodid ciliate Pseudoplatyophrya nana, as well as an abundant fossilized mycelium. The SEM-BSE procedure provided us with ultrastructural details of the fungi and protozoa, especially amoebae and flagellates. In the sandstone samples from Linnaeus terrace, it was possible to identify presumptive diatoms. Ultrastructural details were well-preserved in a fossil Trebouxia-type microalga from Mount Flemming, including the inner chloroplast area normally occupied by the pyrenoid. This fossilized microalga was shown by energy dispersive spectroscopy (EDS) to contain high Si levels in the pyrenoid zone, and high Fe levels in the area corresponding to the chloroplast periphery, peripheric cytoplasm and cell wall. In sandstone from Linnaeus Terrace, fossilized algae showed no central core containing Si, and the entire cell appeared to be completely filled with Al, K and Fe, with Fe most intensely observed within the algal wall.The present observations suggest that a well-preserved cell ultrastructure is the best criterion of biogenicity.