Microsporidia are ubiquitous fungi with genomes that have undergone a strong 
reduction to the extreme cases of Encephalitozoon cuniculi and Encephalitozoon 
intestinalis. Genetic variability within species of the Encephalitozoon genus 
has been reported, with most of the studies based on the internal transcribed 
spacer (ITS) of the rDNA. However, in contrast to the picture of E. cuniculi and 
Encephalitozoon hellem, where different strains have been identified, no genetic 
variability has yet been observed in E. intestinalis. We have analysed tandem 
repeats included in putative coding sequences which could be used as polymorphic 
markers in E. intestinalis. Eight candidate loci (M2, M2A, M3, M5, M7, M7A, M8 
and PTP1) were established and 9 E. intestinalis cultured strains from North 
America, South America and Europe were analysed. M2, M7 and PTP1 nucleotide 
sequences were identical among the different strains and the GenBank sequence. 
In contrast, we observed variants in 4 markers (M2A, M3, M7A and M8) which did 
not correspond to their respective reference sequences. The most noticeable 
finding was that with the M5 marker two genotypes were defined among the 
different strains studied, demonstrating genotypic variability of E. 
intestinalis. Although the diversity described is certainly not high, which can 
be explained by a lower chance of genetic variability in its minimal genome, we 
have demonstrated that polymorphisms actually exist in E. intestinalis. 
Epidemiological studies using this genetic marker should now be conducted to 
elucidate the genetic variability in E. intestinalis and improve our knowledge 
of the epidemiology of this microsporidia.