Gametogenesis drives the maturation of germ cell precursors into functional gametes, facilitated by interactions with the niche environment. However, the molecular mechanisms, especially in invertebrates, remain incompletely understood. In this study, the gonadal microenvironment and gametogenic processes in the Pacific oyster, a model for diffuse gonadal organization and periodic gametogenesis, are investigated. We combine single-nucleus RNA-seq and bulk RNA-seq to analyze gonadal microenvironments in oysters. Twenty-three male and nineteen female gonadal cell clusters are identified, revealing four male and three female germ cell types, alongside follicular cells in females and Sertoli/Leydig cells in males. The NOTCH and BMP (bone morphogenetic protein) signaling pathways play a significant role in the male germline niche, suggesting similarities with mammalian germ cell microenvironment. This study offers valuable insights into germ cell developmental transitions and microenvironmental characteristics. Display omitted •Single-nucleus sequencing provides insights into the cell types in the oyster gonad•Diverse germ cells identified, revealing oyster gametogenesis nuances•NRG, VISFATIN, and SEMA6 pathways aid niche-to-germ communication•NOTCH and BMP pathways play vital roles in male germline niche Wildlife reproduction; Developmental biology; Aquatic biology; Transcriptomics