Nanomaterials exhibit different interesting physical, chemical, electronic and magnetic properties that can be used in a variety of biomedical applications such as molecular imaging, cancer therapy, biosensing, and targeted drug delivery. Among various types of nanoparticles, super paramagnetic iron oxide nanoparticles (SPIONs) have emerged as exogenous contrast agents for in vitro and in vivo deep tissue imaging. Here, we propose a facile, rapid, non-toxic, and cost-effective single step green synthesis method to fabricate eugenate (4-allyl-2-methoxyphenolate) capped iron oxide nanoparticles (E-capped IONPs). The magnetic E-capped IONPs are first time synthesized using a medicinal aromatic plant, Pimenta dioica. The Pimenta dioica leaf extract was used as a natural reducing agent for E-capped IONPs synthesis. The crystalline structure and size of the synthesized spherical nanoparticles were confirmed using the x-ray diffraction and electron microscopic images respectively. In addition, the presence of the functional groups, responsible for capping and stabilizing the synthesized nanoparticles, were identified by the Fourier transform infra-red spectrum. These nanoparticles were found to be safe for human cervical cancer (HeLa) and human embryonic kidney 293 (HEK 293) cell lines and their safety was established using MTT[3-(4, 5-Dimethylthiazol-2-yl)-2, 5-Diphenyltetrazolium Bromide] assay. These green synthesized E-capped IONPs display a distinct absorbance in the tissue transparent near-infrared (NIR) wavelength region. This property was used for the NIR photothermal application of E-capped IONPs. The results suggest that these E-capped IONPs could be used for deep tissue photothermal therapy along with its application as an exogenous contrast agent in biomedical imaging.