The kingdom of fungi comprises an enormous range of live styles and genetic variability. Different genomics approaches offer possibilities to investigate species diversity and ecological function of fungi. In this thesis I present improvements of metabarcoding methods for aquatic fungi and the application of whole genome sequencing and transcriptome sequencing to an exclusively aquatic fungus. Beside the standard metabarcoding marker for fungi, the ITS (internal transcribed spacer) region, the eukaryotic rRNA operon contains two other markers, the SSU (small subunit) and LSU (large subunit), that are also often used for metabarcoding. When choosing a metabarcode there is a tradeoff between high variability for fine grain species delineation and high conservation for good primer binding and high level classification of novel species, which are not represented in reference databases. In the work presented in chapter III, we investigated the possibility to use the information from the more conserved 5.8S sequence, that is part of many amplicons used for ITS2 sequencing. It is normally discarded, but we used it as a complementary marker to ITS2 and showed that it can improve classification of novel species with an incomplete reference database. In chapter IV this is taken one step further by using third generation sequencing to sequence the full ITS region together with the more conserved SSU and LSU in the same amplicon. This gives us the option to use different markers with different databases for classification in parallel and to circumvent the trade-off between high variability and high conservation. Fungi are ecologically very important decomposers of lignocellulose from plant biomass. The occurrence and expression of gene families for the degradation of lignin from lignocellulose has been extensively studied with whole genome and transcriptome sequencing in terrestrial, but not in aquatic fungi. In the work presented in chapter V, we used whole genome and transcriptome sequencing to investigate differential gene expression in the exclusively aquatic fungus Clavariopsis aquatica when grown on media with more and less lignin rich carbon sources and investigated the expression patterns of peroxidases, laccases and other protein families involved in plant biomass degradation. This observed up-regulation of laccases, peroxidases and genes from the cytochrome P450 super-family, as well as other gene families involved in cellulose and hemicellulose degradation, strongly suggests that C. aquatica is able to modify lignin to some extent; perhaps in order to facilitate the utilization of lignocellulose as a carbon and energy source.