Objective We examined the relation between Apolipoprotein E ε4 allele (ApoE ε4) genotype and functional connectivity measured by Electroencephalography (EEG) in patients with Alzheimer’s disease (AD) and patients with subjective complaints (SC). Methods We included 43 patients with AD (age (SD)=74.2 (4.0), m/f=22/21; 30 of ApoE ε4 carriers) and 21 patients with SC (age (SD)=73.2 (5.2), m/f=13/8; 7 ApoE ε4 carriers) for this study. Resting state EEGs were recorded in all subjects. Synchronisation likelihood (SL) between local cortical areas was compared in the alpha and beta band according to ApoE ε4 status and diagnosis. Results ApoE ε4 carriers had higher SL values in lower and upper alpha band, in both diagnostic groups. In upper alpha band and beta band AD patients had lower SL than patients with SC, was irrespective of ApoE status. Conclusion The effects of AD and ApoE ε4 on functional connectivity are opposite and independent. Significance The observed increase in SL in both AD and patients with SC carrying ApoE ε4 suggests a strong genetic impact of ApoE ε4 on brain function.