Relative warps analysis was used to explore the patterns of variation in the shape of silica scales of the freshwater algal flagellate Mallomonas striata (Synurophyceae). Two data sets were analysed: individual worldwide reported scales and the scales of a single population from Trnová pond in the Czech Republic. The comparison of hyperplanes delimited by relative warps analysis of both data sets documented the striking similarity of the two morphospaces, indicating the importance of variation related to the position of individual scales on the cell body. However, there was a higher variability in the worldwide scales set and the analysis of group mean shapes differences revealed the variation in scales morphology in relation to infraspecific identification - M. striata var. striata or M. striata var. serrata - whose body scales have been considered identical so far.