Retrotransposable elements (RTEs) are highly common mobile genetic elements that are composed of several classes, and make up the majority of eukaryotic genomes. The “copy-out and paste-in” life cycle of replicative transposition in these dispersive and ubiquitous RTEs leads to new genome insertions without excision of the original element. RTEs are important drivers of species diversity; they exhibit great variety in structure, size and mechanisms of transposition, making them important putative components in genome evolution. Accordingly, various applications have been developed to explore the polymorphisms in RTE insertion patterns. These applications include conventional or anchored PCR, and quantitative or digital PCR with primers designed for the 5′ or 3′ junction. Marker systems exploiting these PCR methods can be easily developed, and are inexpensively used in the absence of extensive genome sequence data. The main the inter-repeat amplification polymorphism techniques include IRAP, REMAP and iPBS for PCR amplification with a single or two primers.