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Sugarcane is an economically important crop grown for sugar and bioethanol. Most commercial varieties are hybrids of the noble cane Saccharum officinarum and its wild relative S. spontaneum. Sugarcane breeding in the Philippines is focused on the development of new varieties with higher sucrose content and resistance to major fungal diseases. Evaluation of parents for crossing depends on the knowledge of the genetic diversity of the available sugarcane germplasm. In this study, the genetic diversity of 54 local and foreign sugarcane varieties selected from the local germplasm was evaluated through genotyping-by-sequencing (GBS) using diversity arrays technology (DArT). Single nucleotide polymorphisms (SNPs) and silico-DArT (presence/absence) dominant markers were developed using DArT-Seq method, which employs genome complexity reduction method using methylation-sensitive restriction enzymes (REs) and highthroughput next-generation sequencing (NGS). Polymorphism information content (PIC) values of resulting SNP markers range from 0.009 to 0.5 with an average of 0.195, while Silico-DArT markers have PIC values from 0.02 to 0.5 with an average of 0.271. Silico-DArT markers were considered more informative based on higher average reproducibility, call rate, and PIC values. Cluster analysis and principal coordinate analysis using scoring data from SNP and silico- DArT markers showed low-sucrose varieties grouping separately from commercial hybrids developed in the Philippines. However, observed genetic distances among varieties genotyped indicate moderate to high genetic relatedness within the local germplasm, especially among commercially-available varieties in the country. DArT-Seq genotyping was successfully used in analysis of genetic diversity among current commercial varieties and can be a useful tool in the evaluation of new breeding materials for the development of more improved varieties. [ABSTRACT FROM AUTHOR]