Membraneless RNA granules are essential for germ cell development, yet their subcellular molecular characteristics remain poorly understood in fish. In this study, the Balbiani body (BB) and perinuclear dense body (PDB) in oocytes of leopard coral grouper were isolated using laser capture microdissection (LCM), followed by integrated smart-seq2 and DIA proteomics analyses. Ultrastructural observations showed that PDB appeared in oogonia and persisted throughout oocyte development, whereas BB formed in primary oocytes and gradually expanded into the cytoplasm. Integrative analysis of smart-seq2 and DIA proteomics revealed relatively limited transcriptional variation within BB but pronounced dynamic changes in PDB, accompanied by clear differences in protein composition between the two structures. Functional enrichment indicated that BB was mainly associated with RNA storage and cytoskeletal organization, whereas PDB was enriched in RNA processing and regulatory pathways. Known germline regulators, including piwi, tdrd family members, and buc, exhibited structure-specific expression patterns. Furthermore, ddx6 and igf2bp3 were identified and validated as candidate markers, showing dynamic redistribution from perinuclear regions to BB during oocyte development. These findings reveal distinct molecular features of BB and PDB and provide new insights into subcellular RNA regulation in fish oocytes.