All humans have two types of DNA:

Mitochondrial DNA (mtDNA) that is passed down only from the mother and is very similar in all of us because it is just some nuts-and-bolts instructions for how cells work, and

Nuclear DNA (nuDNA) that is passed down from both parents and is the part that makes us the unique individuals that we are.

In 2003 Trace Genetics lab in California took samples from the Starchild Skull and from the human female skull reportedly found with it. The human skull and Starchild Skull are both 900 years old and have been exposed to the same conditions since death, so they should both have the same levels of DNA contamination and degredation, making the female skull a perfect control sample.

The lab recovered both mtDNA and nuDNA from the human skull on the first attempt. She is 100% human and her DNA is haplogroup A. Haplogroups are like blood type but instead it is "DNA type". Haplogroup A means she was of Native American descent.

The lab attempted to recover mtDNA and nuDNA from the Starchild Skull, but despite six attempts and various adjustments to try to get a result, they were only able to recover mtDNA. From that DNA they were able to determine that the Starchild Skull contains human DNA belonging to haplogroup C, another Native American haplogroup, and that the Starchild Skull and the female skull are not genetically related.

The controversy begins with the inability to recover nuDNA. The test Trace Genetics used was the gold standard at the time, but it can recover only human DNA. If there is DNA in the sample that is not human or virtually identical to human, the test will not find it. The nuDNA was easily recovered from the human control skull, and therefore should have been easily recovered from the Starchild Skull. However this did not happen, no human nuDNA could be recovered from the Starchild Skull. This led to a lot of speculation that it may have had a human mother and non-human father (e.g. alien), and there is still a lot of confusion on the internet about this matter.

With the benefit of hind sight and some hints from subsequent preliminary DNA findings, Lloyd Pye believed that the Starchild Skull's strange DNA results indicate it could a new species entirely. Some sections of its DNA appear to be similar enough to human to be found by human DNA tests, and other sections seem too different to register on a test for human DNA.

DNA testing has advanced so much that now it is no longer necisarry to test for specific types of DNA, you can simply remove all DNA from the sample, strip out the contamination, and piece together the DNA that remains. This technique is really the only way to identify DNA that is not yet known to science, and it is the method used to recover the neanderthal genome, among others. The Starchild Project feels this type of DNA testing is the only way to get a definitive answer, and continues to explore every opportunity to have this testing done.