As far I know SSCP will be better.... you can have a look on the following journals for more clarification. Thanks  

http://www.sciencedirect.com/science/article/pii/S0167701205003489

http://www.ncbi.nlm.nih.gov/pubmed/17229479

I can also suggest to go trough clone libraries, if from mixed population, and Sanger sequencing if they are just few of them. If you have isolates, juste amplify and sequence from both sides. PCR and Sanger sequencing are now cheap enough and will give you the real full information about the species you are working on more than DGGE/SSCP/TGGE/RFLP, etc.

I hope this help,

bests

Giuseppe

Thanks Rokib Hasan.

I have a question for you. To use SSCP, Is there  bp limits?

Mr Giuseppe D'Auria Thank you for your excellent answer.

all PCR product sequences of bacteria with Sanger sequesing can be done like NGS or no?

Shahnaz Zare, Fragment length can affects SSCP analysis. For optimal results, DNA fragment size should fall within the range of 150 to 300 bp, although SSCP analysis of RNA allows for a larger fragment size (Wagner, 2002). Tthe presence of glycerol in the gel may also allow a larger DNA fragment size at acceptable sensitivity (Kukita et al., 1997).

Be aware about the following issues too if you use SSCP...

•  Single-stranded DNA mobilities are dependent on temperature. For best results, gel electrophoresis must be run in a constant temperature.
• Sensitivity of SSCP is affected by pH. Double-stranded DNA fragments are usually denatured by exposure to basic conditions: a high pH. Kukita et al. found that adding glycerol to the polyacrylamide gel lowers the pH of the electrophoresis buffer--more specifically, the Tris-borate buffer--and the result is increased SSCP sensitivity and clearer data (1997).

Dear Rokib Hasan

Thanks for attention and Help.