The coral Madracis myriaster is one of the most important reef builders in deep-water habitats of the Caribbean Sea, offering refuge to numerous species of fish and invertebrates. In this study, we developed genomic resources for M. myriaster. Using a low-coverage short read sequencing strategy, this study estimated the genome size, repetitive genome content, annotated and quantified repetitive elements, assembled the 45S rRNA DNA operon, and characterized in detail the mitochondrial genome of M. myriaster. The haploid genome size estimated using a k-mer strategy was 615–697 Mbp, which is within the range reported for scleractinian corals. Repetitive genome content estimates using different word sizes (= k-mers) indicated that 53–65% of the genome of M. myriaster comprised repetitive elements. A relatively large number of the discovered repetitive elements could not be annotated. Taking into account only annotated repetitive elements, the most common were classified as Satellite DNA which were more abundant than Class I-LINE, Class I—Penelope, and Class II (DNA transposons)—Subclass 2 Maverick mobile elements. Less abundant repeat element families included Class I-LTR Ty3 retrotransposons, Class II-Subclass 2-Helitron mobile elements, Class I-LTR-Bel-Pao, and Class I-DIRS mobile elements. The nuclear ribosomal operon of M. myriaster was assembled into a single contig that contains, in the following order: a 5′ ETS [length = 1200 bp (partially assembled)], ssrDNA (1800 bp), ITS1 (233 bp), 5.8S rDNA (158 bp), ITS2 (204 bp), lsrDNA (3616 bp), and 3′ ETS [827 bp (partial sequence)]. The mitochondrial genome of M. myriaster is 17,044 bp long and encodes 13 protein-coding genes, 2 transfer RNAs, and two ribosomal genes. Based on protein-coding genes, the phylogenetic position of M. myriaster was examined. These new genomic resources are of utmost relevance to improve the understanding of the biology of M. myriaster and for the development of conservation plans in this reef-forming deep-water coral.