Here's an abstract about a couple of ancient Jomon genomes from the recent OIST Ancient DNA Symposium in Japan.
Hideaki Kanzawa-Kiriyama, Nuclear Genome Analysis of Ancient Japanese Archipelago Humans
The Jomon period, characterized by chord-marked potteries, lasted from ~16,000 to <3,000 years before present (YBP), and abundant human skeletal remains have been excavated from shell mounds and other sites throughout the Japanese Archipelago. However, their genetic origin and the relationships with modern populations are largely unknown. Here we determined 10% and 80% of the genomic DNA sequences from two Jomon individuals, excavated at Yugura cave site, Nagano, and Shitsukariabe cave site, Aomori, respectively, and compared their genome sequences with worldwide populations. We found a unique genetic position of the Jomon people who had diverged before the diversification of most of present-day East Eurasian populations including East Eurasian Islanders. This indicates that Jomon people were a basal population in East Eurasia and genetically isolated from other East Eurasians for long time. However, their genetic affinities to modern East Eurasians are uneven. The heterogeneity might be a hint to clarify human migration and gene flow in East Eurasia after the divergence of Jomon ancestors.
Hopefully the full paper and genomes are published soon. It'll be interesting to see how these Jomon individuals compare to Western European Hunter-Gatherers (WHG) like Loschbour and Ancient North Eurasians (ANE) like MA-1.
Update 17/01/2015: In fact, the author of this abstract analyzed a variety of Jomon samples, including the two mentioned above, as well as an Upper Paleolithic individual from Ryukyu, for his doctoral thesis back in 2013. The thesis is freely available here.
Update 09/02/2016: The paper is now available and open access at Human Genetics. See here: A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan