Does Cryptosporidium DNA has introns? If so, check if your primers bind to the exon-exon junctions or to two different exons which are separated by introns. I am assuming here that you are using cDNA as a positive control.

thanks Mohsen for your co-operation, I'm really using cDNA as a positive control but I'm predicting that Cryptosporidium DNA has intron since my PCR approach targeting 18s rRNA. in addition,  most of eukaryotic protozoan DNA have got introns within their genome 

 Regarding my primers, I think they bind with the exon position because the DNA was working well in the first time after extraction but when I return back to amplify another products from the same DNA, no band was appearing on  the gel  (no amplification )

So are you saying the first primer set worked, but the second primer set did not work? Every primer set has different PCR parameters even with the same DNA.

THANKS ANDREW. Actually my concerns are not about the primers. The issue is that the PCR working well in the first attempt, but when I need to generate another products from the same DNA samples using the same primers, it dose not work. it seems surprising but that is what happend