This paper reports on findings from two data sets in chemistry learning; one from a multidisciplinary project on teacher lead whole-class teaching, and one from a small-scale study on teacher students’ animations of chemical reactions. The data was analysed as to the use of pictorial language in relation to atoms and ion formation with an intention to shed light on students’ scientific understanding as well as their enculturation into the disciplinary discourse (e.g. Halliday & Martin, 1993; Lemke, 1998; Rogoff, 1990).  Theoretically we draw on social semiotics (e.g. Halliday, 1978; Kress, 2003) allowing analyses of language use in its widest sense, comprising verbal language, images, action, gestures, etc. (e.g. Kress et al., 2001; Lemke, 1998), though here with a main focus on verbal language.  In both learning contexts, we identified common disciplinary metaphors as well as more occasional metaphors. By the use of SFG-analyses (Halliday and Matthiessen, 2004) we also noted more “hidden” metaphoric use, with particles, atoms, and ions being humanised with intentions and feelings. Also, we identified interesting patterns as to the ways students use metaphors to sort out difficulties in understanding chemical processes. The study has implications for the design of classroom practices, not the least as regards possibilities to use meta-discussions to enhance a more reflective use and understanding of the gains and losses around analogies; both as regards teaching material and student-generated analogies (see Haglund, 2013).