Agrostis stolonifera L. and Agrostis capillaris L. differ in their susceptibility to both Sclerotinia homoeocarpa and Rhizoctonia solani fungal pathogens.  There is building evidence that miniature inverted-repeat transposable elements (MITEs) are involved in the regulation of stress responsive gene pathways.  This class of transposable elements has been described in Agrostis, and the first MITEs identified in the species were isolated from a limited set of sequence data.  In the present study, next generation sequencing was done on random sheared genomic libraries from A. capillaris, A. canina, and two A. stolonifera genotypes.  This sequencing yielded 632,420 reads totaling 323 Mb of sequence data, significantly more than was previously available in Agrostis.  Each library was subjected to transposable element finding by the software tools RepeatMasker and FindMITE.  No significant differences were observed between libraries in the transposable elements found by RepeatMasker.  The software program FindMITE identified a total of 18,265 candidate MITEs, which were further placed into families based on conserved terminal ends.  Comparisons between all members of the families across species identified several species specific MITEs.  Species-specific MITEs are interesting because transposition may be induced upon hybridization generating variation that can be used by breeders.  It has also been shown that genetic markers are easily developed from MITEs, which could be used to validate hybridization, particularly in wide-crosses.