Azolla mexicana Presl, a heterosporous aquatic fern, consistently sporulates under routine culture conditions, producing both megasporocarps and microsporocarps in abundance. As a prelude to studies on germ plasm preservation, gametogenesis, embryogenesis, and efforts to establish interspecific hybrids, methods were developed to isolate and separate the reproductive structures. Fertile sporophytes were agitated to release the sporocarps. During this process mature microsporocarps ruptured to release microsporangia. A series of stainless steel sieves, ranging from 1130 to 200 μm in pore size, was used to separate megasporocarps and microsporangia from sporophyte debris and immature microsporocarps. Purified preparations of megasporocarps and microsporangia were obtained using sorbitol step gradients.