Dimpled phosphatic microspherules, contradictorily associated with conodonts, are widely distributed in strata ranging in age from the Cambrian to Carboniferous. These microspherules have attracted much attention from palaeobiologists and were suggested to be ‘conodont pearls’, ‘conodont otoliths’ or ‘fish otoliths’ due to their similar chemical composition and co‐occurrence with conodonts or fish teeth. However, these hypotheses are still highly controversial. Here, we report ‘checks’, ‘rhythmic growth patterns’ and ‘sub‐diurnal increments’ from growth annuli of the Late Devonian phosphatic microspherules from South China, on the basis of quantitative microstructure analysis. The annulus width of phosphatic microspherules becomes narrower with increasing radius. These microstructural characteristics of growth annuli are most typical indicators of modern animal otoliths. In addition, a maximum value of about 90 annuli is encountered from all the specimens. We propose that these microspherules are essentially phosphatic otoliths, which might have been secreted by a specific kind of marine organisms with very short lifespans (less than 90 days). Furthermore, the sudden enrichment of phosphatic microspherules in the late Frasnian may represent a biological response of short‐lived animals to ecological crisis such as ocean eutrophication.