Transposable Elements (TEs) abundance is usually correlated with genome size and organisation. TEs shape genomes and are a source of genetic variations and evolution. Two main defence mechanisms against DNA repeats and particularly TEs are known in fungi, RIP (Repeat-induced point mutation) and MIP (Methylation Induced Premeiotically). Both mechanisms rely on DNA methylation. RIP operates during the sexual cycle. It is an efficient process able to irreversibly inactivate multi-copy sequences by mutating methylated C into T at high rate. MIP involves the methylation of C bases from repeated sequences. We took advantage of the recent burst in fungal genome sequences to evaluate the impact of RIP and MIP on TEs through a comparative analysis. We have searched and annotated TEs from different fungal genomes using a standardized strategy based on the REPET package. This analysis provides a dataset of all TE families with their consensus with and genomic copy sequences. We developed a workflow using RIPCAL to search for TE mutations produced by RIP as well as all dinucleotide bias associated with RIP mutations or other C into T mutation associated process. The results show a strong correlation between the massive TE invasions and RIP deficiency. In addition, we found traces of novel dinucleotide bias in TE abundant genomes, probably associated with MIP-like gene. Finally, the comparative analysis of genes involved in the RIP and MIP silencing mechanisms revealed a strong correlation between dinucleotide abundance patterns and the presence/absence of RIP/MIP genes.