Histological observations represent an important application to directly characterize the structure of tissues and locate host-associated and invasive microorganisms. Histological approaches have been widely employed in studies of the physiology, pathology and ecology of corals. However, the conventional preparation of histological sections requires decalcification of coral samples to remove the hard skeletal structure in a series of acid or EDTA solutions over a weeks’ period, causing potential disturbances in coral structures on prepared slides. In this study, we present an alternative method to prepare thin sections from undecalcified frozen coral tissues, which has been developed for retaining the structural integrity of histological sections including skeleton. Cross sections of normal and diseased (rapid tissue necrosis and black band disease) coral specimens prepared with this method displayed the complete structure of the coral fragments including soft tissues and skeleton structure at microscopic scales, thereby clearly showing the orientation of damaged tissues and associated microorganisms in relation to skeletal structures. This study demonstrates that the present cryosectioning method without the need for decalcification is a highly effective tool for in-depth understanding of coral tissue/skeleton interactions.