Currently, most studies focus on the spatial distribution patterns of selenium (Se) and its fractions in the horizontal surface soils with much less attention paid to their vertical distribution patterns. The investigation about their distribution patterns in soil profiles can further elucidate their migration and transformation paths. Here, total Se and its fractions in tundra soil profiles were quantified by sequential chemical-extraction method and hydride generation-atomic fluorescence spectrometry, to explore the Se distribution patterns and their relationships with penguin or seal population dynamics in maritime Antarctica. Total Se contents were one order of magnitude higher in penguin colony soil profiles than in seal colony and normal tundra. The vertical distribution patterns of total Se were in accord with those of total carbon (TC), total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP) and total sulfur (TS), and total Se levels showed significant positive correlations with historical penguin or seal population proxies obtained from Q-mode factor analysis. Organically bound Se (Seob) and residual Se (Sere) were the dominant fractions with proportions close to 80%, whereas bioavailable Se were the lowest among all fractions. Significant positive correlations of Seob with total Se, TC, TOC, TN, TP, and population proxy indicated that historically high penguin population size and their guano input promoted Seob accumulation. Our results showed that historical penguin and seal population dynamics and their guano input had an important effect on the distribution patterns for total Se and their fractions in soil profiles. This study provides critical information that is useful to understanding Se biogeochemical cycles and the impact of penguins and seals in coastal Antarctica.