We report here the source apportionment of atmospheric soil microorganisms and higher plant metabolites based on chemical markers (hydroxy fatty acids: FAs) in the snowpack samples collected from Mount Tateyama in central Japan during spring 2009 (N = 6) and 2011 (N = 7). A homologous series of β‐hydroxy FAs (C9–C20), constituents of Gram‐negative bacteria (GNB), in snowpacks clearly suggest a long‐range atmospheric transport of dust‐associated bacteria followed by scavenging by snowflakes. Similarly, higher atmospheric abundances of α‐(C16–C32) and ω‐(C9–C30)‐hydroxy FAs in the snow layers containing Asian dust revealed contributions from soil microbes and higher plant epicuticular waxes. Moreover, covariation between the concentrations of hydroxy FAs and water‐soluble Ca2+ (dust tracer), together with calculated air mass backward trajectories, demonstrated their source regions such as the Taklamakan Desert, Gobi Desert, and Loess Plateau. A close match of molecular distributions of hydroxy FAs (with the predominance of ω‐ and β‐isomers) is noteworthy between snowpack (present study) and springtime aerosols from Chichijima Island in the western North Pacific (WNP). This observation suggests a “below‐cloud scavenging” of transported dust particles and associated soil microbes in the East Asian outflow by snowflakes. These distributions are, however, contrary to those observed in the fresh snow samples from Sapporo, northern Japan (predominance of α‐hydroxy FAs), which could be explained by “in‐cloud” microbial oxidation processes. This comparison, therefore, provides additional insights regarding the aeolian transport of soil microbes in the East Asian outflow to the WNP, which has not been available.