A series of dyes 2-5 based on 5-thienyl-2,1,3-benzothiadiazole and 5-thienyl-2,1,3-benzoselenadiazole cores were synthesized as near-infrared-emitting two-photon-absorbing fluorophores. Fluorescence maxima wavelengths as long as 714 nm and quantum yields as high as 0.67 were realized. The fluorescence quantum yields of dyes 2-4 were nearly constant, regardless of solvent polarity. These diazoles exhibited large Stokes shifts (>110 nm) and high two-photon figure of merit. Cells incubated on a 3D scaffold with probe 4 (encapsulated in Pluronic micelles) exhibited bright fluorescence, enabling 3D two-photon fluorescence imaging to a depth of 100 μm.