Plasmodium has a very low GC content. Check your primers for specificity and annealing temperature.

Hi Julian,  I am using the annealing temp used in most publications is 45 degree

Can you be more specific. Are they not working or giving the wrong band sizes  or too many band and do you have any additives eg dmso, betaine in your reaction mix . What is your cycling conditions ?

Thanks Paul, they are giving wrong bands, have a look at the primer sequence. 

Primary Amplification

5' TTTATGATGGAACAAGTCTGC3'

5' AGTATATACATCGCTAACAGA3'

Secondary amplification

 5'GAAATGTAATTCCCTAGATATGGAATATT3'

5'TTAATTTCCCAAGTAAAACTATTAGAGCTTC3'

The cycling conditions  for both are as follows

95⁰C /5min

95⁰C/30s

50⁰C/30s for primary and 45⁰C for secondary

65⁰C/45s 40 cycles

72⁰C/ 5min

Thanks Paul, they are giving wrong bands, have a look at the primer sequence. 

Primary Amplification

5' TTTATGATGGAACAAGTCTGC3'

5' AGTATATACATCGCTAACAGA3'

Secondary amplification

 5'GAAATGTAATTCCCTAGATATGGAATATT3'

5'TTAATTTCCCAAGTAAAACTATTAGAGCTTC3'

The cycling conditions  for both are as follows

95⁰C /5min

95⁰C/30s

50⁰C/30s for primary and 45⁰C for secondary

65⁰C/45s 40 cycles

72⁰C/ 5min