The patch was fragmented as a part of technological development several years ago and i need to check whether those species are reproductively isolated or not.
The best method will be to for population genetics based on neutral markers like SSR or SNP and then use various population genetics software for data analysis. As they are fragmented you should observe high genetic differentiation among two populations. You can even observe rear/private alleles in these populations.
I suggest using RadSeq - a relatively new next generation DNA sequencing technique that is cost effective and results in a tremendous amount of data in the form of Single Nucleotide Polymorphisms. These can be quite informative at the level of genetic differentiation you are targeting.
How many generations have gone by since the development? If the number of generations since development is low, and the population sizes are large, there may not have been enough time for genetic differentiation to build up to a level where molecular methods will help to answer your question (regardless of the kind of marker you choose).
My first thought would be to look on GENBANK for existing genetic resources for the species. Ideally there will be some microsatellites identified. For small projects, despite the promise of next generation sequencing approaches, this is currently probably the most efficient way to quantify ecological-time-scale population differences.
You might get better resolution using something like RadSeq, MiSeq, etc., depending if it is necessary for your question and whether you have the funds.
I'm a gradualist so yes-no questions don't much excite me. But, to be constructive, let me suggest a very interesting recent paper, published on line but not yet in print in Evolution, on genetic and morphological divergence among highly contiguous populations of the Island Scrub Jay. You may find both their results and methods informative.
Discontinuous distribution is well known in marine taxa. Since majority of taxonomical works are based on morphology I wonder how one can delineate individuals of two populatons by genetic studies.
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