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Size differentiation has been considered an important phenomenon in evolution, and in situ speciation was hypothesized in the past for the parapatric subterranean Western Australian Diacyclops Kiefer, 1927 species from the alticola-group, based on morphological evidence. Aims of this study are to: derive their preliminary molecular phylogenies based on mitochondrial (12S) and nuclear (18S) genes; test if morpho-species are supported by molecular data; examine monophyly of the alticola-group; and test whether the size differences evolved in situ after colonization by a single ancestral species or resulted from different phylogeny. Analyses of the 12S sequences reveal at least six well defined clades, each corresponding to one morpho-species. The divergences are very high between all species, suggesting only a remote relationship, with those between sympatric species with significant size difference being in excess of 27%. Surprisingly, all analyses show very high bootstrap values for the clade formed by two cosmopolitan surface-water species, Diacyclops bisetosus (Rehberg, 1880) and D. bicuspidatus (Claus, 1857), despite numerous morphological differences. The 18S dataset also supports only a remote relationship between Diacyclops scanloni Karanovic, 2006 and two other Western Australian members of the alticola-group: D. humphreysi s. str. Pesce & De Laurentiis, 1996 and D. sobeprolatus Karanovic, 2006. Preliminary analyses suggest absence of in situ speciation and parallel evolution in the Western Australian Diacyclops, interspecific size differentiation being a result of different phylogeny. The alticola-group may be polyphyletic, and we recognize morphological characters that define two main lineages. A possibility of cryptic speciation in the cosmopolitan D. bisetosus is also suggested, and several sequences of Diacyclops available from GenBank are recognized either as contamination or misidentification. [ABSTRACT FROM AUTHOR]