Impact of transposable elements (TEs) on genome architecture and evolution stems from their mobility, which ultimately can lead to modifications in the genome including functional disruption and alteration in gene expression. In fungi, TEs genome coverage is extremely variable from one species to another. Rust fungi (i.e. taxonomical order Pucciniales) represent the largest group of obligate biotrophic plant pathogens in the Kingdom Fungi, with more than 8,000 estimated species. The Pucciniales are notorious for their extremely large genome size (from 80Mb to more than 1Gb compared to < 50Mb on average in fungi) with higher gene and TE contents compared to closely related species within the subphylum Pucciniomycotina. For instance, the 1.2Gb diploid genome of the Asian soybean rust fungus, Phakopsora pachyrhizi is composed of >93% of TEs and contains more than 22,000 genes. Here, we investigate the landscape and evolutionary history of TE invasions in the genomes of 11 Pucciniales species compared to four species within the subphylum Pucciniomycotina. We used the REPET pipeline to detect and annotate TEs in order to determine the coverage and composition of TEs within Pucciniomycotina genomes. We found an enrichment of LTRs (Gypsy) and LINE retrotransposons in all genomes of rust fungi, indicating that these elements are the main contributors to genome size expansion in the Pucciniales. An in-depth analysis of retrotransposons insertion ages, based on applying LTR Kimura distance, revealed that most retrotransposons have proliferated less than two million years ago in the genomes of the Pucciniales. Our study indicates a shift in the genomic landscape of Pucciniales shaped by distinct transposable element activity during the recent history of Pucciniomycotina.