The animal superphylum Lophotrochozoa exhibits the greatest disparity of body plans in the animal kingdom, ranging from giant squid to microscopic worms. Among these are the charismatic Mollusca (e.g., snails, and octopus), the medically important Platyhelminthes (e.g., human schistosomiasis), and the familiar Annelida (e.g., earthworms) among many more. Resolving evolutionary relationships within Lophotrochozoa has been difficult due to their likely ancient and rapid radiation. Furthermore over half of the phyla within Lophotrochozoa are microscopic making obtaining the necessary amounts of high molecular weight DNA challenging. Recent advances in molecular biology have made it possible to obtain high quality transcriptomes from a single meiofaunal animal. However, as the entire animal must be used for DNA/RNA extraction, multiple sources of contamination (e.g., gut contents, epibionts, and symbionts) are sequenced as well. These contaminants can be challenging to detect, but are potentially important contributors of non-phylogenetic signal. We are developing a contaminant-aware workflow for phylogenomics of non-model organisms. Newly sequenced reference genomes from this understudied clade will be thoroughly purged of contaminants considering read coverage, GC content, and BLAST hits. Gene models from decontaminated genomes will be compared to potentially contaminated transcriptomes with OrthoFinder and PhyloPyPruner and erroneously inferred “paralogs” best explained by contamination will be purged using our novel software. Utilizing both supertree and supermatrix approaches we aim to further resolve relationships within Lophotrochozoa.