Diabetes management is reliant on consistent and accurate monitoring. Low patient compliance for the standard finger prick test along with its intermittent nature may lead to undetected highs and lows. In 2014, poor glycemic control caused 207,000 hospitalizations from hyperglycemia and 245,000 hospitalizations from hypoglycemia in the US. The implementation of continuous glucose monitors (CGMs) can provide a more thorough illustration of blood glucose level fluctuations. Currently, there are several transcutaneous CGMs produced by Abbott, Dexcom, and Medtronic along with a fully implantable option by Eversense. Improvements to both the sensitivity and size of CGMs are being studied by our group through the development of a competitive binding, FRET-based, glucose biosensor that is fully implantable and probed optically with an external “watch-type” device. In previous work, our group has successfully developed an assay, but due to the near-UV excitation wavelength range, there are limitations in decreased skin penetration depth along with excess noise due to autofluorescence of the tissue. In this work, we investigated the FRET response through skin samples of both Blue (APTS) and near infrared (NIR) (Alexa Fluor 700 and 750) dyes. These dye samples were encapsulated within previously reported hollow, cylindrical, thermoresponsive hydrogel membranes and the fluorescence intensity signals were compared when placed beneath thin and thick (0.87 and 1.85 mm) rat skin samples. The FRET response of AF-700 and AF-700 was measured when placed beneath thicker skin samples of both lighter and dark pigmentations. The results indicate that the use of NIR dyes is needed to allow for a reasonable implantation depth for the implantable biosensor.