High throughput sequencing technology has emerged as a significant tool for discovery of genome-wide markers, which are valuable resource for marker-assisted breeding and integrated genetic improvement of aquaculture species. Unfortunately, for eukaryotic species with large genome size, it remains costly to obtain genome sequences and to develop genomic resources. Climbing perch, Anabas testudineus is one of the most promising aquaculture and climate resilient candidate species, as it can survive in low oxygen water, adaptability to hypoxia, ammonia and other adverse environmental conditions. In the present investigation, genomic resources such as mitochondrial genome, SSRs and SNPs have been developed in a single go by adopting low depth genome sequencing. A total of 45 individuals from three different geographical regions of India were selected and subjected to sequencing in Illumina Nextseq 500 platform. The longest contig 16603bp obtained from the best assembled genome from the single individual was predicted and aligned with the best match obtained on blasting against the NCBI nr database and annotated using MitoFish mitochondrial genome annotator tool to obtain the complete mitogenome of climbing perch (KX950694). Also, a total of 1,05,693 microsatellite sequences have been identified using MISA tool out of which 90514 were di-repeats, 11187 tri-repeats, 2558 tetra, 1024 penta and 410 were hexa nucleotide repeats. A total of 49 GB raw data was generated for SNP identification. Using VDAP-GUI pipeline a total of 10 million SNPs were identified taking the climbing perch draft genome sequence (Accession no. OOHO00000000. 2) available in the GenBank, as reference. The present study demonstrates that low depth genome sequencing can be used as an efficient method for marker discovery in non-model species. The resources generated here will be useful for population diversity studies, marker assisted selection, and genome-wide association studies.