A number of parasites are known to infect the reproductive system of fish resulting in grossly visible lesions. Some of these have the reproductive tract as their primary predilection site, whereas others are less tissue-specific infecting the different visceral organs including the gonads or reproductive tracts. The most reported types of parasites that infect the reproductive system of fish are microsporidia, myxozoans and nematodes. Microsporidian parasites of the genus Glugea are acquired by the host fish when they either ingest free spores from the water column or consume infected aquatic invertebrates. The gross clinical presentation of fish that have gonads infected by microsporidia is dependent on whether they are xenoma- or non-xenoma-forming microsporidia. There is minimal cell reaction to the developing non-xenoma-forming microsporidia and it is only when mature spores are released from the ruptured oocyte that phagocytosis occurs. Neoplasia of the male and female reproductive organs are considered rare but have been reported in a diverse variety of fish.