Fear and frustration are two emotions thought to frequently contribute to problem behaviour, often leading to relinquishment. Inferring these emotions is challenging as they may present with some similar general signs, but they potentially require different treatment approaches to efficiently address the behaviour of concern. Although behavioural assessment frameworks have been proposed, it is largely unknown how clinical animal behaviourists (CABs) assimilate information about the emotional state of an animal to inform their behavioural assessment. In other fields (such as both in human and veterinary medicine), the use of intuition and gut feelings, without the concurrent use of an assessment framework, can lead to higher rates of error and misdiagnosis. Therefore, this study used semi-structured interviews of ten CABs and qualitative methods to explore the ways they conceptualise, recognise and differentiate fear and frustration in dogs. Although interviewees perceived fear and frustration as negative affective states that lead to changes in an animal's behaviour, there was little consensus on the definition or identification or differentiation of these emotions. The use of a scientific approach (i.e., hypothesis-driven and based on falsification of competing hypotheses) for behavioural assessment was highly variable, with individual assessment processes often characterised by tautology, intuition, circular reasoning and confirmation bias. Assessment was typically based on professional judgment, amalgamating information on interpretation of communicative signals, motivation, learning history, breed, genetics and temperament. Given the lack of consensus in the definition of these states, it is clearly important that authors and clinicians define their interpretation of key concepts, such as fear and frustration, when trying to communicate with others.