In Drosophila ovaries, germline stem cells (GSCs) divide asymmetrically in the germaria to produce daughter GSCs and cystoblasts. Single cystoblasts differentiate to form germline cysts with 16 germline cells, all of which are connected by the fusome, a vesiculated structure critical for oocyte specification. We here show that histone H3K9 methyltransferase dg9a is associated with spectrosome/fusome formation in the germarium; dG9a13414 mutant ovaries have disorganized spectrosome/fusome in about half the germaria, with reduced levels of hu-li tai shao and α-SPECTRIN proteins. We found that the amount of germline cells within cysts was reduced and that oocyte determination often failed in egg chambers of the dG9a13414 mutant ovaries. These results suggest that a mutation in dG9a gene gives rise to anomalous spectrosome/fusome structures, which in turn lead to faulty germ-cell development in Drosophila ovaries.