This book explores the intersection of molecular biology, genomics, and ecology to redefine our understanding of parasitic organisms and their management. Beginning with the application of -omics research in platyhelminth parasites of fish, demonstrating how genomic and proteomic data are essential for understanding host-parasite dynamics and developing novel vaccines and treatments to support sustainable aquaculture. The focus then shifts to the complex internal ecosystems of parasites, and examining how their associated microbiomes-comprising bacteria, fungi, and viruses-influence parasite fitness, virulence, and host interactions. Finally, the book highlights the genus Entamoeba, delving into how how next-generation and long-read sequencing technologies have revolutionized the identification of cryptic species and improved epidemiological surveillance for pathogens like E. histolytica. Together, these chapters provide a modern framework for parasitology through the lens of advanced genetic tools and ecological integration. · Direct application to global food security · Integration of the "holobiont" concept · Genetics-based redefinition of parasite taxonomy