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High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. In this study, we developed and validated a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific amplicons using PacBio circular consensus sequencing. We focused on the wheat microbiome as a proof-of-principle and demonstrate unprecedented resolution for the wheat-associated Pseudomonas microbiome and the ubiquitous fungal pathogen Zymoseptoria tritici. Our approach achieved an order of magnitude higher phylogenetic resolution compared to existing ribosomal amplicons. We show that the designed amplicons accurately capture species and strain diversity outperforming full-length 16S and ITS amplicons. Furthermore, we tracked microbial communities in the wheat phyllosphere across time and space to establish fine-grained species and strain-specific dynamics. To expand the utility of our approach, we generated pangenome-informed amplicon templates for additional key bacterial and fungal genera. The strain-level microbiome profiling enables the tracking of microbial community dynamics in complex environments and is applicable to diverse ecological niches. Overall, our work demonstrates how pangenome-informed amplicons overcome limitations in phylogenetic resolution to unravel microbial strain diversity and dynamics.