Neandertal is our closest known relative and also an archaic hominid reserving the richest fossils. Whether the Neandertals exchanged their DNA with modern human or not is a matter of debate on the modern human origin. The progresses on the mitochondrial and nuclear genomes of Neandertals in recent years were reviewed in this paper. Recent study has revealed possible genetic contribution of Neandertals to the modern human to some extent, which arose the rethinking of modern human origin. The experiences gained in the research on Neandertals will benefit the study on archaic hominids, unravel the mystery of modern human origin, and enrich the relative theoretical systems in evolutionary biological field.