Silkworm is an economically significant insect. It holds value in sericulture, protein synthesis, and as a model species for pest-destroying strategies. The construction of molecular maps and genome sequencing by utilizing Whole Genome Sequencing, Next Generation Sequencing, Third Generation Sequencing, and long reads from Pacbio, Bac, or Fosmid libraries has helped in studying its population genetics and developing it as a reference organism for lepidopteran order. Sequencing of mitochondrial DNA and cytochrome b gives insights into silkworm domestication and separation on the Phylogenetic tree of Bombyx Mori and Bombyx Mandarina species. The impact of various environmental stresses and coping mechanisms is being adopted by silkworms at various life stages. Humidity affects cocoon coloration, larvae growth, and the quality of produced cocoon. We have also reviewed genetic engineering tools available to induce double-strand breaks DSBs in the silkworm DNA sequence; highlighting the drawbacks of Zinc Finger Nucleases and Transcription Activator-like (TAL) Effector Nucleases (TALENs) and the advantages of utilizing the CRISPR tool for editing genes at various targeted sites. This review discusses molecular tools that facilitate genetic engineering in silkworm species and the status of silkworm molecular genetics research to enable the study of gene expression patterns in environmentally stressed conditions.