Silicide-based photonic materials have attracted a great deal of research interest due to their compatibility with the well-developed silicon technology. Extensive efforts have been made for the synthesis and characterisation of these materials. This paper covers some aspects of the microstructural and crystallographic characteristics of ion beam synthesised silicides such as the semiconducting iron and ruthenium silicides, using transmission electron microscopy. A previously predicted new orientation relationship has been found to exist between the Si substrate and ion beam synthesised βFeSi2 nanocrystals, which are free of 90° rotational order domain boundaries.