High levels of biodiversity and endemism in ancient lakes have motivated research on evolutionary processes in these systems. Drill-core records from Lake Titicaca (Bolivia, Peru), an ancient lake in the high-elevation Altiplano, record the history of climate, landscape dynamics, and diatom evolution. That record was used to examine the patterns and drivers of morphological evolution of an endemic species complex of diatoms in the lake, the Cyclostephanos andinus complex. In an attempt to delineate species within the complex based on morphology, no discernible evidence was found for species separation based on an ordination analysis of multiple characters, but multiple populations were detected based on the distribution of valve size in individual samples. Likelihood modeling of phyletic evolution showed that size evolved through punctuated change. Correlation of size trends with environmental variables indicates that C. andinus size responded to regional environmental change driven by global processes that influenced Lake Titicaca by affecting lake level and thermal stratification.