The present investigation is based on detailed taxonomical analyses combining light microscopy (LM), scanning electron microscopy (SEM) and critical reviews of publications and type material. This method revealed a higher number of diatom taxa than that reported for the Altiplano, reports that are based on LM and SEM, but force-fitting the taxa into their European relatives. It also became evident that some taxa often reported from the Altiplano do not occur or are less common in this region and that misidentifications are the consequence not only of force-fitting, but also of misinterpretation of the original protologues and illustrations (taxonomic concept drift). These findings have important repercussions on past palaeoecological assessments for the Altiplano, which have been based on ecological information for taxa developing in ecosystems of highly contrasting conditions. Here we present the case of three araphid diatoms, which were reported as known taxa from Europe and elsewhere, but in fact correspond to taxa described as new for the Altiplano or unpublished taxa. It is recommended that: (1) a flora for this region is developed utilizing sound microscopical data and reviewing pertinent type material, (2) key common taxa used for past palaeoecological studies in the Altiplano are reviewed using a taxonomically thorough and critical method, and (3) future palaeoecological studies for the Andes are supported by prior detailed taxonomical analysis.