Both the hippocampus and amygdala are early vulnerable brain regions in the development of Alzheimer's disease (AD). However, previous studies mainly focused on characterizing the hippocampus in the pathophysiology of AD, leaving the amygdala less explored. The study was designed to characterized the structures and functions of neurons in the hippocampus and amygdala of young (2, 3 and 4 months of age) APP/PS1 double transgenic (Tg) mice. Pavlovian fear conditioning task and novel object recognition test were used to assess amygdala- and hippocampal-dominant memory functions. Single neurons in the hippocampal CA1 and CA3 regions and the basolateral amygdala (BLA) were labeled by fluorescent dye injection to determine dendritic arborization. Impairment of the amygdalar-associated cued fear learning manifested earlier than did the hippocampal-associated contextual learning. Diminution of dendritic arbor complexity was observed in the neurons of BLA as early as 2-months-old, while the dendritic arbors of neurons in the hippocampal CA1 and CA3 regions were relatively intact. BDNF signaling pathways were reduced in the amygdala, but not in the hippocampus, of young Tg mice. Reduction of 5-HT levels and elevation of Aβ levels in the amygdala precedes those in the hippocampus. Neurodegeneration occurs earlier in the amygdala than in the hippocampus.