Aspergillus affinis (section Circumdati) is a novel ochratoxin A (OTA)-producing species found in submerged riparian decomposing leaves. However, very little is known about its role on the breakdown of plant debris and its ability to degrade carbohydrate polymers. Moreover, its OTA biosynthetic pathway has not yet been explored. In the present paper, we investigated the gene encoding the extracellular alpha-amylase (amyAa) of A. affinis within the evolution of the Aspergillus lineages in relation to the possible use of this enzyme in starch processing. The novel amyAa, despite being related to branches of the Aspergillus species of the sections Terrei and Flavi, formed a distinct phylogenetic branch, which may be of outstanding importance from a biotechnological point of view. Moreover, we identified the polyketide synthase gene (pks) putatively required for the first step of OTA biosynthesis in A. affinis. This otapks was examined in relation to a limited number of orthologous genes available from Aspergillus species of the sections Circumdati and Nigri. Our study highlights the importance of otapks as target genes in the treatment of ochratoxigenic Aspergillus species on a more comprehensive evolutionary basis.