In this study we investigated Diphenylalanine (FF), which is well known to form complex self-assembled structures, including peptide microtubes, nanowires, and nanofibers, with morphologies depending on the amino (NH3-) and carboxylic (COO-) terminal modifications. The aim of this study was to demonstrate whether fluorescent TMPyP and Rhodamine B are both noncovalently incorporated into FF peptide nanotubes (PNTs) during self-assembly when analyzed using spectroscopy and fluorescence methods. Seven samples were prepared and analyzed for this experiment, including FF, TMPyP and Rhodamine B, either alone or in various combinations. Four techniques were employed to analyze the samples. UV-vis spectroscopy was conducted to identify and quantitate the molecules of interest in the solution. Fluorescence spectroscopy was conducted to measure total fluorescence in sample solutions and fluorescence microscopy established how much of the fluorophores were incorporated into FF micro/nanotubes during self-assembly. Lastly a Scanning Electron Microscope (SEM) was utilized to provide images of FF, TMPyP and Rhodamine B. Results obtained from this experiment showed that Rhodamine B was readily and stably incorporated into the walls of FF nanostructures, whereas TMPyP did not display as much affinity to FF micro/nanostuctures as Rhodamine B. It is recommended that in future experiments, TMPyP samples be scanned using fluorescence microscopy at a different range (from 675 nm to 720 nm instead of at 420nm), in order to visualize how much reduced TMPyP is noncovalently incorporated into FF nanotubes.