The choice between the organs used for pollination is made through a detailed study of crossing barrier. For instance, if lack of stigma receptivity or slow pollen tube growth are the crossing barriers, pollination can not be carried out on stigma, but instead placenta or ovules will have to be used for pollination. The bisexual flowers need to be emasculated and bagged before ovaries are excised for in vitro operations.

After fertilization, the ovules or ovaries are transferred to a fresh medium for seed development. In contrast to the above situation in plants (where ovule or ovary is used for in vitro fertilization), the in vitro fertilization in humans and other animals always involve fusion of an isolated egg with a sperm in test tube . However, till recently plant gametes could not be isolated and fused in a test tube.

The technique of in vitro pollination and fertilization is also useful in overcoming self incompatibility, where selfing is desired but can not be achieved by conventional method of bagging bisexual flowers. As we know self incompatibility does not allow fusion of male and female gametes from the same plant, even though the gametes are fertile.

It is attributed to barriers at the level of pollen germination and/or pollen tube growth, so that fertilization can be affected, if in vitro pollination is carried out directly on the ovule or on the ovary after removing the stigma and style.