The amygdala and raphe nuclei, which play crucial roles in mood regulation, are influenced by serotonergic neurotransmission. Alterations in this neurotransmission are associated with mood disorders. Therefore, using immunohistochemistry and quantitative methods this study was designed to evaluate potential alterations in the expression of serotoninergic markers in the amygdala and raphe nuclei of mice with oestrogen receptor β (ERβ) knock out which exhibit increased anxiety as evidenced by reduced locomotion and increased thigmotaxis. These alterations could either contribute to heightened anxiety or serve as a compensatory strategy for reducing it. The results show that in ERβ knock‐out mice, 5‐HT1B expression is significantly increased in the amygdala, while 5‐HTT expression is significantly decreased in both the amygdala and raphe nuclei. Furthermore, ERβ deficiency does not affect TPH2. In conclusion, serotonin signalling is altered in the amygdala and raphe nuclei of ERβ knock‐out females. It seems that an increase in 5‐HTT levels has been associated with reduced anxiety, whereas a decrease in 5‐HT1B receptors may encourage fear. However, further studies are required to determine the exact role of ERβ in anxiety‐related behaviour.