Fungal species play extremely important roles in ecosystems. Clustered at the 
base of the fungal kingdom are Microsporidia, a group of obligate intracellular 
eukaryotes infecting multiple animal lineages. Because of their large host 
spectrum and their implications in host population regulation, they influence 
food webs, and accordingly, ecosystem structure and function. Unfortunately, 
their ecological role is not well understood. Present also as highly resistant 
spores in the environment, their characterisation requires special attention. 
Different techniques based on direct isolation and/or molecular approaches can 
be considered to elucidate their role in the ecosystems, but integrating 
environmental and genomic data (for example, genome architecture, core genome, 
transcriptional and translational signals) is crucial to better understand the 
diversity and adaptive capacities of Microsporidia. Here, we review the current 
status of Microsporidia in trophic networks; the various genomics tools that 
could be used to ensure identification and evaluate diversity and abundance of 
these organisms; and how these tools could be used to explore the microsporidian 
life cycle in different environments. Our understanding of the evolution of 
these widespread parasites is currently impaired by limited sampling, and we 
have no doubt witnessed but a small subset of their diversity.