Microalgae are highly valued for their rapid biomass production and metabolite synthesis, as well as their abundance of beneficial compounds. They have a variety of applications, including serving as the primary ingredient in biofuels, functional foods, and cosmetics. The genus Picochlorum, which was established to represent the unique characteristics of “Nannochloris-like” algae, exhibits rapid growth and a high salt tolerance. The morphology, molecular phylogeny, and fatty acid composition of an unspecified Picochlorum strain KCTC AG61293 found in Korean coastal waters were investigated. The strain exhibited a unique cell morphology and reproduction type compared to other Picochlorum species, as determined using light microscopy, fluorescence microscopy, and field emission scanning electron microscopy (FE-SEM). The vegetative cells were elongated and cylindrical in shape, underwent binary fission, and possessed a parietal chloroplast. A molecular phylogenetic analysis using nuclear small subunit ribosomal RNA sequences showed that Picochlorum sp. (KCTC AG61293) belongs to the Picochlorum clade and is closely related to the genus Nannochloris. Compared to other reference species, Picochlorum sp. (KCTC AG61293) had higher levels of saturated fatty acids (SFAs) and alpha-linolenic acid (ALA). The increased levels of SFAs and ALA suggest that Picochlorum sp. (KCTC AG61293) may be a promising candidate for biofuel production and other industrial uses.