Many eukaryotic histidine-to-aspartate (His-Asp) phosphorelay systems consist of three types of signal transducers: a His-kinase (HK), a response regulator (RR), and a histidine-containing phosphotransfer intermediate (HPt). In general, the HPt acts as an intermediate between the HK and the RR and is indispensable for inducing appropriate responses to environmental stresses. In a previous study, we attempted but were unable to obtain deletion mutants of the <italic>ypdA</italic> gene in order to characterize its function in the filamentous fungus <italic>Aspergillus nidulans</italic>. In the present study, we constructed the C<italic>ypdA</italic> strain in which <italic>ypdA</italic> expression is conditionally regulated by the <italic>A. nidulans alcA</italic> promoter. We constructed C<italic>ypdA</italic> strains with RR gene disruptions (C<italic>ypdA-sskA</italic>Δ, C<italic>ypdA-srrA</italic>Δ, and C<italic>ypdA-sskA</italic>Δ<italic>srrA</italic>Δ). Suppression of YpdA induced by <italic>ypdA</italic> downregulation activated the downstream HogA mitogen-activated protein kinase cascade. YpdA suppression caused severe growth defects and abnormal hyphae, with features such as enhanced septation, a decrease in number of nuclei, nuclear fragmentation, and hypertrophy of vacuoles, both regulated in an SskA–dependent manner. Fludioxonil treatment caused the same cellular responses as <italic>ypdA</italic> suppression. The growth-inhibitory effects of fludioxonil and the lethality caused by <italic>ypdA</italic> downregulation may be caused by the same or similar mechanisms and to be dependent on both the SskA and SrrA pathways.