Habitat loss is the most likely threat to Phodilus prigoginei.
The Congo Bay-Owl is one of only two species in the genus Phodilus, the other being the Asian (or Oriental) bay-owl Phodilus badius, a widespread but little known lowland forest bird from northern India to Borneo. It is a rare species, having defied many attempts to relocate it since the type-specimen was collected in 1951 in a grass clearing in montane forest at Muusi, 2,430 m, in the Itombwe Mountains, Zaïre.
Owing largely to the remoteness of the area and political disturbances, there has been little scientific work at Itombwe since the early 1960's.
A Congo bay-owl was almost certainly observed on a tea estate in Burundi in the mid-1970s. Calls of an unidentified owl, structurally similar to that of the Asian bay-owl were heard in Nyungwe forest, Rwanda, in 1990; this forest is at serious (but remediable) risk. In 1996, a small Congo bay-owl was captured in Itombwe, the first positive occurrence in over 40 years.