Repetitive elements within genomic DNA are both functionally and evolutionarily informative. Discovering these sequences ab initio is computationally challenging, compounded by the fact that selection on these repeats is often relaxed; thus sequence identity between repetitive elements can vary significantly. Here we present a new application, the Monomer Identification and Isolation Program (MiIP), which provides functionality to both search for a particular repeat as well as discover repetitive elements within a larger genomic sequence. To compare MiIP’s performance with other repeat detection tools, analysis was conducted for synthetic sequences as well as several α21-II clones and HC21 BAC sequences. The primary benefit of MiIP is the fact that it is a single tool capable of searching for both known monomeric sequences as well as discovering the occurrence of repeats ab initio, per the user’s required sensitivity of the search. Furthermore, the report functionality helps easily facilitate subsequent phylogenetic analysis.