We demonstrate a multimodal imaging methodology to probe the nanoscale environment of cells. The system combines partial-wave spectroscopic (PWS) microscopy and spectroscopic photon localization microscopy (SPLM). PWS quantifies the nanoarchitecture of cells with sensitivity to structures between 20 and 200 nm. SPLM is a newly developed super-resolution imaging technique based upon the principles of single-molecule localization microscopy and spectroscopy. In addition to allowing super-resolution imaging, SPLM provides inherent molecular-specific spectroscopic information of targeted structures visualized when dyes are used. Combining both of these modalities into a single instrument allows nanoscale characterization of the super-resolution molecular imaging provided by SPLM as it relates to nanoscale structural information provided by PWS. As an example, we labeled RNA polymerase in HeLa cells and showed correlations between the locations of the RNA polymerase visualized by SPLM and the nanoscale structure of the chromatin measured by PWS. Such information is crucial in understanding the role of specific molecules in regulating the chromatin structure and gene expression. More broadly, this instrument can give insight into the molecular pathways of diseases and therapeutic treatments of those diseases, while simultaneously showing the effects on chromatin topology.