There are many techniques that could be used such different types of Molecular markers to assess the Molecular diversity

Data Comparative Assessment of Genetic Diversity in Tomato Cultiv...

You can also use retrotransposons based Molecular markers technique

Article Retrotransposon-based molecular markers for assessment of ge...

Dear colleagues,

 If need there are russian articles concerning zebra and quagga mussels: for example - 

Natural hybridization of two mussel species Dreissena ..... I. S. Voroshilova et al.

CLONAL AND POPULATION RAPD VARIATION ..... Korsunenko A.V. et al, 

Comparative analysis of the structure and fauna of endosymbionts of communities of two dreissenid species............E. G. Pryanichnikova et al 

Article Comparative Analysis of the Structure and Fauna of Endosymbi...

Article Natural hybridization of two mussel species Dreissena polymo...

Article Clonal and population RAPD variation of cercariae obtained f...

Dear Asif Laldin,

Please find attached article

Voroshilova I.S., Artamonova V.S., Makhrov A.A., Slyn'ko Yu.V. 2010. Natural hybridization of two mussel species Dreissena polymorpha (Pallas, 1771) and Dreissena bugensis (Andrusov, 1897) // Biology Bulletin. v. 37. No. 5. p. 542-547.

Best wishes

Alexander Makhrov

Severtsov Institute of Ecology and Evolution

Russian Academy of Sciences

Leninsky prosp. 33,

Moscow, 119071, Russia

e-mail: [email protected]

From preliminary bioinformatic analysis it seems there is not a great degree of variation between markers such as 16s 18s, 28s. 

May need to start looking for SNPs and other such small variation. Does anyone else have any comments on this?

Dear colleague,

I think about it you can ask to Dr. Irina S. Voroshilova directly.

(As I know she has the thesis  concerning this problem).