Specie complex with multiple genetic clades is frequently observed using mitochondrial makers in pelagic copepods. However, reproductive isolation among clades is not fully understood due to low sequence variations in common nuclear markers, and genome-wide method with high taxonomic resolution is require to reveal species boundary in problematic taxa. Pleuromamma abdominalis is pelagic copepods with high genetic diversity and one of ideal taxa to study species complex. Here, 31 individuals of P. abdominalis with six mtCOI clades were collected in the western subtropical North Pacific. For obtaining Single Nucleotide Polymorphisms (SNPs), two genome-wide methods were used: multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and double digest restriction site associated DNA sequencing (RAD-seq).