One of the main rapeseed pathogens, Leptosphaeria maculans, is mainly controlled by using cultivars with quantitative and/or specific resistance genes against the pathogen. The influence of resistant genotypes on the targeted pathogen is expected. However, this work considers the pathogen in a broader environment, interacting with the whole microbiota locally present. With new sequencing technologies, it is now possible to describe the microbiota associated with a pathogen and analyze how it can be modified by the plant genetic background and over time.Here, we used metabarcoding sequencing of two barcode genes in duplex for fungal identification: the Internal Transcribed Spacer (ITS) region and the single-copy Actin gene . The generated datasets were used to describe the fungal mycobiota present on different rapeseed tissues sampled in fields (leaves, stems and residues) at key time points (sampling date) in the L. maculans life cycle over two cropping seasons. This work was done on isogenic rapeseed cultivars carrying or not the Rlm11 resistance gene The whole data set first demonstrated the complementarity of ITS and Actin barcodes to identity and quantify, respectively, fungal species, including the main rapeseed fungal pathogens. The dynamics of pathogens over each cropping season fits our knowledge about their epidemiology. The main factors structuring fungal community were the sampling date (SD), and the cropping season (CS).The plant genotype (PG) explained only a small percentage of fungal diversity variation. These two last effects (CS and PG) increased when the dataset anaysed was divided per SD or CS. An alternation of species between the different ecological niches (leaves, stems, residues) was visible, with variations among the two sampling years. In conclusion, the introgression of a resistance gene to a fungal pathogen in Brassica napus does not seem to be the main driver of the mycobiome structure whatever the ecological niche.