Termites (Isoptera) are known from all tropical, subtropical, and some temperate regions of the world (Jones and Eggleton, 2011) with more than 3000 described species (Engel and Krishna, 2004). While most often associated with economic damage, less than 3% of all species are known to cause damage to manmade structures, forestry and agriculture products (Edwards and Mill, 1986 and Logan et al., 1990). The use of pathogens for microbial control of economically important termites has been considered a popular subject of research but efforts have been largely ineffective (Chouvenc et al., 2011). Most evaluations have been conducted with generalist pathogens (mainly bacteria, fungi and nematodes) isolated from non-termite hosts as few naturally occurring pathogens have been identified. While it appears microbial control holds limited promise, it is evident that the diversity and role of natural pathogens in termites are poorly known. In this report a new genus and species of microsporidia is described from termites collected in Ecuador based on host, morphology and 16S rDNA sequence data.