According to Hong et al. (2005), the major allergen Alt a 1 facilitates identification to the species level, but later studies showed that it is not sufficient within some sections like the small-spored section Alternaria (Dettman & Eggertson, 2021; Hong et al., 2005; Woudenberg et al., 2015). When using molecular barcode markers, a combination of several loci is necessary. The most commonly used markers are ITS, GAPDH, RPB2, TEF1 and Alt a 1 (e.g., Kokaeva et al., 2022; Woudenberg et al., 2014), and most studies with a multilocus phylogeny employ these five or subset of them, with or without additional, less common loci like endoPG, histone H3, calmodulin and OPA 10–2 (e.g., Adhikari et al., 2020; Bessadat et al., 2021; Ding et al., 2019; Landschoot, Vandecasteele, Carrette, et al., 2017; Woudenberg et al., 2015). Recently, Dettman et al. developed (Dettman & Eggertson, 2021, 2022) and tested (Dettman et al., 2023) new markers to achieve better identification of small-spored Alternaria.

Nishikawa and Nakashima claim that morphological and molecular phylogenetic data should be complemented by experimental host ranges to achieve an integrated species recognition (Nishikawa & Nakashima, 2020). Genes for host-specific toxins are subject to horizontal gene transfer and some A. alternata pathotypes spontaneously lose their pathogenicity as a consequence of losing their capability to produce the host-specific toxin, so pathotype should not be employed as a character in the taxonomy of small-spored Alternaria (Andrew et al., 2009; Pinto & Patriarca, 2017). Chemotaxonomy, using secondary metabolite profiling for species identification, showed promising results for some species groups like A. infectoria (Andersen et al., 2008; Andersen & Thrane, 1996; Kelman et al., 2020; Zwickel et al., 2018) but not for all sections of Alternaria (Andersen et al., 2015; Zwickel et al., 2018). Secondary metabolite profiles can be combined with morphological and molecular analyses for polyphasic taxonomy (Pinto & Patriarca, 2017). The study by Woudenberg et al. (2015) is also an example for the combination of methodological approaches, as it employed a multilocus phylogeny, whole genome data and transcriptomics (Woudenberg et al., 2015).