Examples of the ocular, digestive gland and brachial end-organ photophores of specimens from all 13 cranchiid genera are described. The cranchiine and taoniine subgroups have different ocular photophore morphologies, but very similar brachial end-organs in adult females. Most taoniines have ocular photophores that contain large numbers of crystalloids, but these are lacking in Helicocranchia and Sandalops. There are no crystalloids in cranchiine ocular photophores, in taoniine digestive gland photophores (Megalocranchia) or in the brachial end-organs of both groups. The cranchiine Leachia atlantica uniquely has one group of photocytes that contain aggregates with some similarities to the taoniine crystalloids. The end-organs of mature females have a glandular structure; the deciduous photocytes are structurally different from those present in the ocular or digestive gland photophores. The reflectors of Sandalops and Megalocranchia contain unusual arrangements of iridosomal platelets. End-organs lack any reflective structures. The comparative anatomy of the photophores supports the separation of the cranchiine and taoniine groups but the ultrastructural detail provides common links between the two.