MethPrimer is a program designed for designing primers for bisulfite-conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation-specific PCR (MSP). The program, based on Primer3, integrates CpG island prediction into the primer design process. It can handle the unique constraints of bisulfite-conversion-based PCRs, such as the requirement for primers to have a sufficient number of non-CpG 'C's in the original sequence to bias the amplification of completely modified DNA. MethPrimer also supports primer selection for COBRA and MS-SNuPE methods with minor modifications. The program is freely accessible via a web browser and is implemented on a Linux platform. It has been tested for its performance and scalability, showing linear execution time with the length of the query sequence. MethPrimer is particularly useful for researchers focusing on well-characterized sequences or regions, such as promoter sequences, and does not require checks for repetitive elements or vector sequences in the input sequences.MethPrimer is a program designed for designing primers for bisulfite-conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation-specific PCR (MSP). The program, based on Primer3, integrates CpG island prediction into the primer design process. It can handle the unique constraints of bisulfite-conversion-based PCRs, such as the requirement for primers to have a sufficient number of non-CpG 'C's in the original sequence to bias the amplification of completely modified DNA. MethPrimer also supports primer selection for COBRA and MS-SNuPE methods with minor modifications. The program is freely accessible via a web browser and is implemented on a Linux platform. It has been tested for its performance and scalability, showing linear execution time with the length of the query sequence. MethPrimer is particularly useful for researchers focusing on well-characterized sequences or regions, such as promoter sequences, and does not require checks for repetitive elements or vector sequences in the input sequences.