Xanthene-based functional dyes have diverse applications in life science and materials science. A current challenge is to develop new dyes with suitable physicochemical properties, including near-infrared (NIR) operation, for advanced biological applications such as medical diagnostics and molecular imaging. In this review, we first present an overview of xanthene-based functional dyes and then focus on synthetic strategies for modulating the absorption and fluorescence of dyes that operate in the NIR wavelength region with bright emission and good photostability. We also introduce our work on aminobenzopyranoxanthenes (ABPXs) and bridged tetra-aryl-p-quinodimethanes (BTAQs) as new xanthene-based far-red (FR)/NIR absorbing/emitting molecules whose absorption/fluorescence wavelengths change in response to external stimuli.