Dear Ankit,
Mitochondrial stains usually involve fluorescently-tagged molecules. However, if you'll choose red-tagged fluorophores, they won't interfere with GFP staining.
It is possible to stain mitochondria via immunocytochemistry. For example, use anti-Cytochrome C Oxidase or anti-TOM20 (stainings that I tried) as primary antibodies and use secondary antibodies conjugated to red fluorophores. Another possibility is prior fixation to use MitoTracker Red CMXRos (Life Technologies), which accumulates as a function of mitochondrial activity and stays after aldehyde-based fixations.
I hope it helps,
Best of luck,
Julia