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The spotted salamander (Ambystoma maculatum) shares a unique endosymbiotic relationship with the unicellular green alga, Oophila amblystomatis. Despite studies isolating and identifying O. amblystomatis in salamander eggs, the taxonomic identity of the alga remains a point of ongoing debate. In this study, the nuclear SSU rRNA gene was used to characterize two well-supported Oophila clades that include lineages identified from past studies in addition to new isolates from the current study. These two clades do not form a monophyletic group and, furthermore, O. amblystomatis appears to be paraphyletic with numerous other chlamydomonad algae. To gain further insight into the biogeographic variation of the host A. maculatum, the mitochondrial ND4 and control gene regions were examined and the phylogeography was observed to be similar to that noted in the literature. Additionally, the response of O. amblystomatis to atrazine and 2,4-dichlorophenoxyacetic acid following 96h exposure and a 96h recovery phase was characterized, as this is a plausible mechanism by which the development of the host salamander could be impaired by herbicides. At the 96h growth rate, no-observed-effect concentrations were 64g/L and 30mg/L for atrazine and 2,4-D, respectively. We observed full recovery ofO. amblystomatis at these concentrations within 96h. These data suggest that atrazine and 2,4-D do not pose a significant risk to the symbiotic algae, or, indirectly, to the host salamander. In conclusion, we recommend a revision of the current taxonomy of O. amblystomatis, and demonstrate the need for species identification and thorough phylogenetic reconstruction in toxicity testing to accurately inform risk assessment.