The first attempts to isolate embryo sacs from ovule tissues date back to the middle of the 20th century (reviewed by Xin and Sun, 2010). Isolation of male and female gametes in combination with expressed sequence tag (EST) sequencing and generation of cDNA libraries subsequently allowed the identification of genes expressed in gametes from maize (Zea mays), wheat (Triticum aestivum), Nicotiana tabacum and Arabidopsis, and from the generative cell from Lilium longiflorum (Dresselhaus et al., 1994; Kumlehn et al., 2001; Xu et al., 2002; Engel et al., 2003; Lêet al., 2005; Sprunck et al., 2005; Okada et al., 2006; Yang et al., 2006; Xin and Sun, 2010; Xin et al., 2011). However, suitable techniques for targeted isolation of almost every cell type of interest from male and female germline lineages were established only recently, based on micromanipulation, fluorescence-activated cell sorting (FACS), and laser-assisted microdissection (LAM) (reviewed by Xin and Sun, 2010; Hu et al., 2011). In addition, a method for the isolation of nuclei from specific cell types (isolation of nuclei tagged in specific cell types, INTACT) has recently been developed (Deal and Henikoff, 2011). In brief, micromanipulation is based on manual dissection of the tissue, sometimes in combination with enzymatic digestions of cell wall components, while FACS sorts cells based on their fluorescence and light scattering characteristics (reviewed by Hu et al., 2011). During LAM, cells or tissue types of interest are isolated with a laser from thin sections of fixed and embedded tissue (reviewed in Day et al., 2005; Nelson et al., 2006). The method was originally developed for the isolation of specific cells from animal tissues (Emmert-Buck et al., 1996) and first used for plant cells only more recently (Kerk et al., 2003; Casson et al., 2005). The INTACT method, on the other hand, uses affinity-based purification of nuclei expressing biotinylated proteins in the nuclear envelope of the target cells (Deal and Henikoff, 2011). The suitability of the different methods for the isolation of individual cells from male and female germline lineages, however, is largely dependent on the cell type of interest and the species used. Male gametophytic cells can be relatively easily isolated, e.g. by osmotic shock and separation by Percoll gradient centrifugation, as successfully applied for uninucleate microspores, binucleate pollen, and sperm cells from Arabidopsis and rice (Oryza sativa) (Table 1; Honys and Twell, 2004; Wei et al., 2010; reviewed by Xin and Sun, 2010). In addition, FACS has been successfully used to sort mature Arabidopsis pollen and to isolate sperm cells from maize and Arabidopsis (Table 1). Micromanipulation has been applied to isolate male Arabidopsis meiocytes (microspore mother cells, MiMCs) (Table 1) and the generative cell of L. longiflorum, but also embryo sacs, female gametes and zygotes from a variety of different species including maize, A. thaliana, O. sativa, Tourenia fournieri and Alstroemeria aurea (Becker et al., 2003; Engel et al., 2003; Pina et al., 2005; Hoshino et al., 2006; Okada et al., 2006, 2007; Chen et al., 2010; Takanashi et al., 2010; Ohnishi et al., 2011; Yang et al., 2011; Libeau et al., 2011; reviewed by Xin and Sun, 2010; Hu et al., 2011). Disadvantages of these powerful techniques, however, are that FACS often requires the use of a cell-type- or tissue-specific marker, as does the INTACT method. Apart from this, FACS, INTACT and micromanipulation may require prolonged handling or treatment with macerating enzymes, such that effects on RNA expression patterns or RNA stability cannot be fully excluded. However, if handling time is kept short, the transcritional program of specific cell types does not appear to undergo substantial changes (Birnbaum et al., 2003). LAM, on the other hand, is applicable for cell-type-specific isolation with little cross-contamination for a variety of purposes, because: (i) the use of specific markers is not required, and (ii) the tissue is fixed prior to any manipulation, such that transcriptional profiles are unaffected by the handling (Wuest et al., 2010; Schmidt et al., 2011; Schmid et al., 2012). The downside of LAM is that it can be very time-consuming, depending on the cell type of interest. Also, the cell type of interest needs to be structurally distinguishable from the surrounding tissue in thin sections and isolated cells may contain minor contamination from neighbouring cells depending on the exact structural organization of the tissue within the section. While the laser beam leaves nucleic acids in the adjacent cytoplasm mostly intact, the thickness of the beam/section, and thus the suitability for the isolation of small cell types, varies with the LAM system used. Laser-assisted microdissection has been successfully applied to profile the cell-type-specific transcriptomes at different developmental stages of the male and female germline in different species, including MeMCs (Schmidt et al., 2011), the three cell types of mature female gametophytes in Arabidopsis (Wuest et al., 2010) and different developmental stages of the male germline in rice (O. sativa ssp. japonica‘Nipponbare’), including pre-meiotic MiMCs, microspores, bicellular and tricellular pollen (Hirano et al., 2008; Hobo et al., 2008; Suwabe et al., 2008; Tang et al., 2010).