The overall population size and trend of the Magellanic Penguin (Spheniscus magellanicus) is uncertain and population estimates are available only for few locations. The last complete census along its central-southern distribution range in Argentina, province of Santa Cruz, was made in the 1990s. This study updates the breeding population size along Santa Cruz. Population estimates were compared with the last complete census, and trends were studied when it was possible. With 353,256 estimated breeding pairs, the overall population in Santa Cruz remained relatively stable after 25 years. The Santa Cruz population represents 31% of the Argentine Patagonian coast population and could represent between 22 and 30% of the species' global population. Colony sizes varied between 9 and 127,492 breeding pairs. Changes in abundance differed among locations, with individual colonies showing increasing, decreasing, or stable trends, which suggests that local factors determine population dynamics. The most significant increases (> 40%) were observed in the southern sector of Santa Cruz. Contrary to what was observed at the north of the distribution range in the province of Chubut, where trends of several colonies were inversely related to colony size, in Santa Cruz most of the largest colonies remained stable or even increased from the 1990s onwards.