Use a combination of morphological character and morphometic measurements from the female fenestral region and the second stage juveniles. What genus are you working on?

Thank you Dr. Rebecca for the nice reply. I am working on cereal cyst nematodes mainly H. flipjevi and H. avenae.

I would recommend the following book which has excellent identification keys-Systematics of Cyst Nematodes (Nematoda: Heteroderinae), Part B.  Please follow the links below.

http://www.brill.com/systematics-cyst-nematodes-nematoda-heteroderinae-part-b

Dear Muhammad

You can separate these two species based on some morphological and morphometrical characters. H. avenae has long and dark cyst and without underbridge in vulval cone. In H. filipjevi, cysts are smaller and brown and you can see a week underbridge in vulval cone.

Thank You Abas for nice suggestion.

@ Rebecca, Unfortunately I do not have the access of this book. It would be nice of you, if you could send me the Chapter where cyst nematodes are mentioned.

@ Abas, what are the attributes of larvae, like stylet length, shape and tail shape etc?

Dear Muhammad

I think there is a high variability in morphometrics and morphology of J2s in this group and in many may be we can not separate them. please see the attachments. I think sequencing of ITS region can be a useful method.  

For the identification you have to go through morphometrics, morphology and molecular ( DNA-RFLP)  for the authentication at species level

Dear Abas, Thank for sending the resources.