Classifying and naming taxa is crucial in all biological sciences, and palaeontology is no exception. With the advent of computer sciences and digitized information, Computer Aided Identification systems are of particular interest to paleo-taxonomists dealing with large fossil collections or sampling. Computer-stored and managed knowledge databases allow the exploration of morphological data themselves, but also their relation with ecological or distribution information. Thus, these databases have plentiful applications in systematics, palaeoecology or palaeoclimatology. Among all tools available, Xper2 is a user-friendly application, which can be used to store, edit, analyse and distribute structured descriptive data. Lately, an online interface (Xper3) was introduced to develop online collaboration and diffusion of knowledge databases. Our contribution aims to introduce this tool and to illustrate its helpfulness in several aspects and issues in palaeontology, by giving relevant examples of applications for palaeobotany: (i) an Icacinaceae database and its application in phylogenetic studies, (ii) PalmID, an online identification tool for modern and fossil palms, (iii) ABIeS, an ongoing project proposing a tool for fossil softwoods identification and (iv) the potential use of Xper2 and Xper3 in paleoclimatic studies based on fossil leaves. Additionally, the relevance of Xper3 in teaching applications and knowledge transfer to the public will be discussed.