Fish scales accumulating in marine laminated sediments can provide a record of population variability of small pelagic fishes. Although some studies have noted signs of scale degradation that could affect estimates of population variability, there are presently no well-developed means to evaluate degradation. We developed several indices as indicators of fish scale preservation in two box-cores that we collected off Pisco (14°S), one at 301 m near the center of the oxygen minimum zone (OMZ), and the other at 201 m near the upper limit of the OMZ. These indices include (1) an index of fish scale integrity (estimate of scale wholeness relative to fragmentation), (2) the fungi-free area of fish scales and vertebrae, (3) the ratio of fish scales to vertebrae (as well as fish scales to vertebrae and bones), and (4) the ratio of whole scales to fragments. We address whether lower numbers of anchovy scales occurring in association with reduced total organic carbon fluxes and higher bottom-water oxygen concentrations are due entirely to lower abundances of anchovy or whether differential preservation of the fish scales in the sediments plays an important role in reduced scale abundances. Comparison of temporal sequences between the two cores provides the means to assess whether there are differences in the preservation of fish scales. The combined indices indicate that the lower numbers of fish scales in the earliest period have been affected by degradation, and to a greater degree in the box-core from 201 meters, which can be subject to higher oxygen concentrations. On the other hand, decadal-scale variations in fish scale abundance within the period of better preservation are unlikely to be caused by degradation. We discuss the utility and drawbacks of different indices of preservation for reconstructing past changes in fish population sizes with fluxes of fish debris and also briefly discuss the utility of these indices to other paleobiological systems.