There is considerable interest in the factors which may explain variation in microbial community assembly processes. In this study, we investigated bacterial community assembly, phylogenetic diversity and the relative role of deterministic and stochastic processes along environmental gradients on Mt. Norikura, Japan. DNA extracted from soil samples collected at a range of elevations was PCR-amplified targeting the V3 and V4 regions of the bacterial 16S rRNA gene, and sequenced using Illumina MiSeq. We hypothesized that elevation would be a strong predictor of phylogenetic community assembly, with communities being more phylogenetically clustered towards higher elevations, due to more extreme physiological conditions. We also hypothesized a greater role of stochasticity at the highest elevations, due to more frequent soil disturbance. Contrary to our hypotheses, we found that the strength of phylogenetic clustering and the role of stochasticity were strongly related to soil pH, with phylogenetic clustering and deterministic processes being strongest at lower soil pH values. Moreover, there was no trend towards stronger influence of phylogenetic clustering and stochasticity in the upper elevations of Mt. Norikura. These results reveal an overwhelming influence of soil pH on phylogenetic community assembly of soil bacteria, even when a range of other environmental gradients are present.