Stramenopiles are a diverse eukaryotic supergroup with considerable genomic information available. Nevertheless, the relationships between major stramenopiles subgroups remain unresolved and incongruent between analyses, in part due to a lack of data from small nanoflagellates that make up much of the genetic diversity of the group, under-represented ochrophyte classes, and a rapid radiation leading to eroded phylogenetic signals in the tree. As a result, assessing genetic diversity and distribution, addressing character evolution, and investigating interactions of these lineages with other organisms are limited. To resolve phylogenomic relationships of stramenopiles, I generated 23 transcriptomes from the most under-sampled subgroups, such as Bigyromonadea, MAST-6, Placididea, and some classes of ochrophytes that had been scarcely represented in phylogenomic data. Of these, 11 are new species of stramenopiles, some of which have helped resolving phylogenomic relationships of Bigyromonadea and the backbone of deep-branching lineages. Some of these species were found to be abundant in sediment sampled across different geographic locations, while others can tolerate a broad range of salinities. I also described behaviours and morphological characters of these species including the ability to form pseudopods and cell-aggregates observed in some bigyromonads. This updated phylogenomic dataset now represents 14 out of 17 classes of ochrophytes and demonstrates robust support for previously contentious or under-tested lineages such as Eustigmatophyceae, Pinguiophyceae, and Olisthodiscophyceae. To address phylogenomic incongruence between multi- or single-gene trees, I explored various gene filtering criteria to identify the phylogenetically informative genes. Selecting genes with long internal phylogenetic branches or removing genes with high levels of phylogenetic noise recovered more topologies that were found in other phylogenomic analyses. Finally, I investigated the only reported case of a prokaryotic endosymbiont found among non-photosynthetic lineages of stramenopiles, in the tiny flagellate Symbiomonas scintillans. Instead of endobacteria, I detected multiple giant viruses related to prasinoviruses. This work demonstrates how little we know about symbioses, particularly in nano- or pico-flagellates. Overall, this thesis highlights complex evolutionary histories of stramenopiles inferred from the most up-to-date phylogenomic tree. This work will inform further exploration into trait evolutions related to niche occupation, morphology, and immunity.