The R package TROM (TRanscriptome Overlap Measure) is a new bioinformatic tool for comparing transcriptomes of biological samples from the same or different species. The comparison is conducted based on testing the overlap of "associated genes" of different samples. The goal is to find clear correspondence patterns among the transcriptomes. The package provides useful functions with flexibility for illustration and customization. Moreover, the package can identify associated gene sets for downstream analyses and can be easily integrated into existing comparative genomic pipelines.