Reflectance spectroscopy has several advantages compared to traditional chemical methods in paleolimnology. It requires little cost, involves minimal or no sample preparation and is rapid. There has, however, been limited use of reflectance spectroscopy in polar paleolimnological studies. This paper explores the application of reflectance spectroscopy to reconstruct historical changes in penguin population size in the maritime Antarctic. Two ornithogenic sediment cores on Ardley Island, Antarctica were analyzed. Penguin droppings and weathered soils were analyzed as reference materials. Principal component analysis and linear mixing modeling were performed on the spectral data to estimate the proportion of penguin guano in the sediments and these values were used to infer historical penguin population numbers. Historical penguin population size versus time, reconstructed from reflectance spectra, and population numbers inferred from previous geochemical analysis of bio-elements, were quite similar. Our results illustrate the feasibility of rapidly inferring historical changes in penguin population size using reflectance spectroscopy on Antarctic ornithogenic sediments. Our findings suggest that this technique has potential for reconstructing past population numbers of other seabirds and mammals using lake sediments influenced by animal excrement.