Abaca (Musa textilis Née) is a diploid Musa species native to the Philippines that is used to produce abaca fibers. The Philippines supplies 85 percent of the world supply for raw fiber, fiber craft, cordage and pulp, which provide livelihood opportunities for 1.5 million Filipinos. Cutting edge molecular markers is needed to support germplasm management and crop improvement of this understudied crop. The objective of the study is to adapt a set of SNP markers from banana and validate the efficacy of the SNP markers for abaca genotype identification. Using a nano-fluidic genotyping platform, we evaluated 384 putative Single Nucleotide Polymorphism (SNP) markers developed for diploid banana (Musa acuminata Colla), based on 62 abaca germplasm accessions. The cross-species transfer of nuclear SNP markers showed a 15.6% success rate, resulting in the selection of 60 polymorphic SNPs. The generated SNP profiles enabled accurate identification of all tested abaca cultivars and detection of homonymous naming mistakes. Cultivars with a background of inter-specific hybrid (e.g. M. textilis x M. balbisiana) were differentiated using multi-variant analysis and Bayesian stratification. These selected SNP markers will be highly useful for downstream applications in abaca industry, including cultivar identification, nursery accreditation, and authentication of abaca product and protection of intellectual property rights.