Insertion sequence elements (ISs) are short transposable DNA sequences that play a major role in genomic rearrangements in bacteria. Despite their importance and pervasiveness, IS-associated genomic architectures - defined by the spacing, order, and relative orientation of ISs - have not been systematically characterized. Here, we present a computational pipeline for identifying IS-associated architectures, from both assembled genomes and long-read sequencing data at single-molecule resolution. Applying this approach to large-scale microbial genomic datasets, we detected both known amplification structures and more complex architectures, uncovered a previously uncharacterized inverted-flank structure, and observed distributions of structural configurations across IS families and bacterial taxa within the analyzed dataset, suggesting associations between some structures and IS families.