To expand on the biodiversity study of the eastern Alpine region of North Tyrol, we investigated silica-scaled chrysophyte flora of unexplored high-altitude Alpine sites. We concentrated mostly on lakes that were 1000–2500 m above sea level; some of them were still partly ice covered. Overall, 27 taxa were recorded at 12 sites, despite 21 sites being sampled altogether. In general, the sites were oligotrophic and species poor. Due to a restricted data set, an extensive analysis was not possible. However, altitude and pH were found to be important variables for explaining species distribution. We described the new species Mallomonas pechlaneri from two of the sampled sites. Mallomonas pechlaneri most closely resembles Mallomonas striata var. striata and M. striata var. serrata; these three taxa are clearly distinguished by bristle morphology and scale shape. The bristles of M. pechlaneri terminate in a bifurcated tip consisting of unequal diverging branches. Scale shape was captured my means of landmark-based geometric morphometries (GM) and evaluated using multivariate statistical analyses. GM methods proved to be an efficient tool to be employed in chrysophycean taxonomy.