The few-celled female gametophyte, or embryo sac, of flowering plants is not easily accessible as it is buried within the sporophytic tissues of the ovule. Nevertheless, it has become an attractive model system to study the molecular mechanisms underlying patterning and cell type specification, as well as fertilization of the two female gametes, the egg and the central cell. While female gametes, zygotes, and early embryos can be manually isolated from the embryo sacs in maize, wheat, tobacco, and rice by micromanipulation, this approach had been considered impossible for the much smaller embryo sac of the model plant Arabidopsis thaliana. Here, we describe a method to isolate living cells from the Arabidopsis female gametophyte by micromanipulation. The manual isolation of egg cells, central cells, and synergid cells is a technique that enables a number of important studies such as cell-type-specific transcriptional profiling or the analysis of DNA methylation profiles. It also offers the possibility to use isolated female gametes for in vitro fertilization studies.