Background <p>Parental contributions to offspring phenotype extend beyond genetic inheritance, encompassing non-genetic factors that influence early development. However, the interplay between maternal and paternal effects remains poorly understood. This study investigates these contributions in Eurasian perch (<i>Perca fluviatilis</i>) — a valuable model to study parental effect in finfishes — by analyzing early life traits and transcriptomic profiles of larvae resulting from crosses between wild and domesticated parents.</p> Results <p>Maternal effects dominated key developmental traits, including hatching success, growth, and swim bladder inflation. Transcriptomic analysis revealed a complex regulatory interplay, with 573 genes under exclusive maternal control, while no genes were solely influenced by paternal input. Maternal-effect genes were primarily associated with metabolic, developmental, and stress-response pathways, shaping early larval physiology. Further analysis identified Eurasian-perch-specific candidate maternal-effect genes, such as <i>crtac1</i>, <i>slc16a7</i>, <i>cox5b</i>, <i>kdr</i>, <i>cald1</i>, and <i>bin2</i>, highlighting their potential role in early development. Although paternal contributions were limited, a subset of genes exhibited conditional paternal influence, suggesting a nuanced parental interplay in gene expression regulation.</p> Conclusions <p>These findings challenge the traditional perspective of strictly coordinated parental contributions, instead revealing a dynamic parental interplay over gene expression and offspring traits. The dominance of maternal effects suggests a primary role in shaping early development, while paternal factors may modulate expression patterns in a context-dependent manner. This study enhances our understanding of parental effects in fish, providing valuable insights for aquaculture breeding strategies and evolutionary biology research.</p>