Mallomonas is one of the biggest genera of Chrysophyta. In total, 37 species and 2 varieties have been recorded in China. Because of their narrow ecological optimum, species of this genus are considered as valuable bioindicators. However, taxonomy of Mallomonas remains unclear. We studied the numerical taxonomy of all the species and varieties recorded in China using Ward’s method and the furthest neighbor method based on 52 morphological characters. Shown in the phylogenetic trees, those species could be divided into two major clusters. One cluster includes 5 small clusters and another includes 2. The results of numerical taxonomy are partially consistent with the traditional ones with some divergences. Furthermore, the diversity of silicified scales including shapes and structures was confirmed as the most important character for identification of Mallomonas species. 1. Introduction The genus Mallomonas, which was created by Perty in 1852, is reported as one of the biggest genera in Chrysophyta [1, 2]. It is comprised of 163 species around the world so far, of which 37 species and 2 varieties are from China [3–14]. Mallomonas are unicellular, free-swimming, freshwater organisms. Because of their narrow ecological optimum, Mallomonas species are considered as valuable bioindicators to both recent and historical environments, as well as for biomonitoring [15–18]. Smol suggested that morphological variability of silica structures within individual species could represent an important piece of information for biomonitoring studies [19]. Therefore, it is important for us to make a clear and reasonable classification system of this genus. The basic taxonomic system of the genus Mallomonas was first established in 1933 and has been modified for several times [20–27]. Nowadays, the genus Mallomonas is traditionally divided into sections and series in mainly the morphology of scales, which is considered as the most important taxonomic character for species identification and the taxonomy of the species [5, 28]. However, we shall be aware that this classification based mainly on resemblances and the difference in the structures of scales and bristles may be highly artificial, because it is still unknown which scale characters are stable enough to be selected as reliable taxonomical markers. Also, since it is hard to collect enough samples of unicellular bodies for molecular analysis, phylogenetic studies that used the molecular data were also difficult for generic taxonomy and phylogeny of the genus Mallomonas. Therefore, the phylogenetic reliability of
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