Arrays composed of BODIPY and hydroporphyrin (chlorin or bacteriochlorin) components feature multiple strong absorption bands across visible and near-IR regions, efficient energy transfer from BODIPY to hydroporphyrin moiety, and strong deep-red or near-IR emission. These properties make such arrays attractive candidates for a variety of applications, particularly in solar energy conversion and biomedicine. In this review, the molecular design, synthesis, and photophysical properties of BODIPY-hydroporphyrin arrays are described. Their applications as fluorescent probes for in vivo imaging are also discussed.