Biological treatments using microalgae represent an environmental-friendly approach to the decontamination of coking wastewater, which contains toxic levels of ammonium; however, few algal species can tolerate such high ammonium levels. In this study, we investigated the morphology, ultrastructure, molecular phylogeny, and physiological characteristics of Parachlorella kimitsuensis sp. nov., a new algal species with high ammonium tolerance. This species was isolated from coking wastewater obtained near a steelworks factory, where the ratio of nitrogen to phosphorus (N/P) exceeded 40, approximately 100-fold that of general culture medium. The growth inhibition test estimated that the effective concentration at 10 % inhibition (EC10) was 3.2 ppm NH4+-N, and the half maximal effective concentration (EC50) was 98.0 ppm NH4+-N, indicating tolerance to fairly high concentrations of ammonium in this species. Parachlorella kimitsuensis has spherical, green cells resembling those of Chlorella species. The major diameter of the cells was 3.7 ± 0.39 μm; cells containing eight autospores appearing in the early logarithmic growth phase were 6.9 ± 0.78 μm in diameter. Molecular phylogenetic analysis showed that the alga was a member of the genus Parachlorella, with 100 % bootstrap support. However, the results of vegetative cell morphology and phylogenetic analyses using 18S rRNA genes were inconsistent with those of other described Parachlorella species. Therefore, we identified the isolate as a new species in the genus Parachlorella. We anticipate that this species will be suitable for biological treatment of wastewater containing high ammonium levels, such as coking wastewater.