Retrotransposons are ubiquitous, generally dispersed components of eukaryotic genomes. These properties, together with their “copy and paste” life cycle that generates insertional polymorphism without need for excision ,makes them widely useful as a molecular-genetic tags. Various tagging systems have been developed that exploit the sequence conservation of retrotransposon components, such as found in their long terminal repeats (LTRs). To detect polymorphisms for retrotransposon insertions, marker systems generally rely on PCR amplification between the terminii and some component of flanking genomic DNA. As complements to various “wet lab” protocols for retrotransposon tagging, in silico bioinformatics approaches are useful for predicting likely outcomes from unsequenced accessions on a basis of reference genomes. In this chapter, we describe protocols for in silico retrotransposon-based fingerprinting techniques using the FastPCR software as an integrated tools environment for in silico PCR primer design and analysis.