The goals were to investigate implicit learning in mild cognitive impairment (MCI), and to determine the relations of implicit learning systems to apolipoprotein E (ApoE) genotype in healthy controls. Elderly controls grouped by ApoE status (ApoE-e4 allele carriers versus ApoE-e4 allele non-carriers) and MCI patients participated in the study. Individuals in all three groups completed both contextual cueing and serial reaction time (SRT) tasks. In the former, people learn to use repeated spatial configurations to facilitate search for a target, whereas in the latter, they learn to use subtle sequence regularities to respond more quickly and accurately to a series of events. Results revealed that healthy elderly individuals carrying the ApoE-e4 allele showed contextual cueing deficits compared to those who did not carry the ApoE-e4 allele. Further, elderly controls carrying the ApoE-e4 allele revealed similar amounts of contextual cueing as the MCI group, while the non-carriers performed better. Sequence learning, by contrast, was uninfluenced by either MCI or by ApoE genotype in healthy controls. This study provides further support for the medial temporal lobe dysfunction and relative integrity of fronto-striatal systems in MCI, and indicates the influence of ApoE genotype on implicit learning even in healthy older individuals without cognitive impairment.