Flying squirrels belong to the subfamily Petauristinae. They are arboreal and nocturnal. They don't actually fly, but slide between trees thanks to a sliding membrane (patagium). This membrane connects the front legs to the hind legs (Parr, 2003). In other words, a hairy, parachute-like membrane extends from the wrist to the ankle. The flaps of skin that connect the limbs to the body provide a wing-like surface. All species have reddish eyes, brighter in large species than in smaller ones which can be quite dim. The subfamily exhibits serious taxonomic complications, with little agreement among mammalian researchers (Parr, 2003). Giant flying squirrels (Petaurista sp.) have the highest diversity in terms of population richness in Southeast Asia. This species is large in size, being on average 422 mm long. The red giant flying squirrel is believed to mate twice a year and the young are generally born in March or August in litters of 2 - 3 (Parr, 2003). The Indochinese ground squirrel (Menetes berdmorei) is a member of the Sciuridae family. The family has only 29 species of 14 genera in Thailand (Lekagul and McNeely, 1977, 1988; Par, 2003). The characteristics of the Indochinese ground squirrel are the black stripe in the central part of the back, two or three black stripes on the sides and the reddish-brown fur on the back (Lekagul and McNeely, 1977, 1988; Par, 2003). Identification, however, is more difficult during the dry season, when the colors are much less vibrant. They have been found throughout Southeast Asia, from eastern Myanmar to Vietnam. As a ground squirrel, it is rarely found in trees, but spends most of its time in the dense undergrowth of rainforests. (Walston and Duckworth, 2008). The size of squirrels varies from species to species. There are three types of...... half of the article ...... at least one restriction enzyme and sequencing of the resulting fragment ends using an Illumina genomic analyzer to sample the genomes of multiple individuals in a population (Baird et al., 2008). The main advantage of RAD is that it provides information for a very large number of loci in the genome and for the same loci in each individual sampled. The current method for accelerating targeted sequencing from ancient and highly degraded DNA includes linking multiplex PCR directly with sample barcodes and high-throughput sequencing. The method offers the possibility of simultaneously generating many kilobases of overlapping sequence data from 31 ancient cave bear (Ursus spelaeus) specimens (Stiller et al., 2010). It seems likely that high-throughput sequencing technologies will offer many advantages for the study of ancient DNA in the future.