An aquatic yeast capable of amorphous selenium nanoparticles (SeNPs) synthesis was isolated and characterized as a novel strain of Rhodotorula mucilaginosa R-8441 based on its morphology and amplification of ITS1-5.8S ITS2 16 rDNA sequence. The effect of various parameters such as precursor concentration, biomass concentration, and time incubation on the biosynthesis of nanoparticles was investigated. A variety of complementary analyses, including Ultraviolet-visible spectroscopy (UV–vis), Field emission scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy (FESEM-EDS), Dynamic light scattering (DLS), Transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), and Powder X-ray diffraction (XRD), were used to characterize the biosynthesized SeNPs. SEM and DLS results showed that the yeast strain could synthesize spherical and rod-shaped SeNPs extracellularly and intracellularly. After 72 h of incubation in the presence of 1 mM selenite oxyanion concentration, monodisperse preparation of spherical shape SeNPs with an average size of 83 nm was obtained. SeNPs have shown rod-shaped particles with an average diameter of 478 nm in the presence of 5 mM selenite stock solution. Besides, TEM results show the intracellular accumulation pattern of SeNPs in cell biomass treated with selenite oxyanion at a concentration of 5 mM after 72 h of incubation.