Since Neanderthals and modern humans split at about 500,000 year ago, it suggests that she did not originate from that divergent. Instead, she represents an unknown hominin lineage, presumably an unknown migration out of Africa. "X-Woman" is too young to be a descendant of Homo erectus (which migrated out of Africa to Asia about two million years ago) yet too old to be a descendant of Homo heidelbergensis.
"Whoever carried this mitochondrial genome out of Africa about a million years ago is some new creature that has not been on our radar screens so far," said co-author Professor Svante Paabo, also from the Max Planck Institute for Evolutionary Anthropology.
Read more about this discovery on BBC News, DNA identifies new ancient human.
Said article can be found on Nature, The complete mitochondrial DNA genome of an unknown hominin from southern Siberia (Krause et al., 2010).
*Edit* Here's a pdf from Nature, Fossil finger points to new human species.