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mechanisms in the ribosomal RNA genes were investigated using Epichloë fungal endophyte interspecific hybrid isolate, Lp1. The two progenitor isolates, Neotyphodium lolii Lp5 and E. typhina E8, were used for comparison. Three areas of homogenisation were examined. The first area involved characterisation of extraordinary length heterogeneity in the rDNA of Lp1. This was shown by Southern analyses on single-spore isolates to be present intragenomically and localised to the intergenic spacer (IGS). Length heterogeneity is not a feature of either progenitor, suggesting it is a consequence of the hybridisation. The length heterogeneity was shown to result from copy number variation of sub-repeats in the IGS, which is consistent with unequal crossing over occurring in the rDNA, suggesting that unequal crossing over plays a role in homogenisation. Multi-variant repeat PCR mapping of the sub-repeat array revealed that the ends of the array behave differently, and biased initiation of recombination is discussed. Several results are not consistent with homogenisation by unequal crossing over and the potential roles of gene conversion and extrachromosomal rDNA circles in homogenisation are discussed. Finally, evidence is presented that suggests the rate of homogenisation is very rapid. A group I intron is present in the 28S rrn gene of Lp1, and is widespread in the Epichloë endophytes. Closely-related introns in other fungal 18S rrn genes provide evidence for intron transposition. The second area involved testing the hypothesis that the presence of one type of rDNA sequence in Lp1 is the result of interlocus homogenisation. CHEF gel electrophoresis revealed that Lp1 and Lp5 have at least five rDNA arrays organised as major and minor loci, an unusual situation in fungi. The organisation in E8 could not be determined. One potential rDNA-DNA junction was cloned but has not been analysed. The final area initially involved testing the hypothesis that interlocus homogenisation of 5