I have tried to isolate DNA from Padina but it is not getting amplified using markers that are working fine for other algal samples. Is there any specific method or precaution which should be followed?
Use Google/Pubmed to find out whether other researchers have had the same problem. Perhaps there is a known Taq Pol inhibitor in DNA preparations from that species? In that case, do serial dilutions of your sample and try them by PCR, to find out whether you can find a sweet spot at which the inhibitor is sufficiently diluted but the DNA is still amplifiable.
I found amplifications I did on shark tissue to be extremely sensitive to magnesium chloride concentrations. No idea if this will apply to Padina samples, but worth considering if the other suggestions don't help!