With the technology of PAGE,the genetic polymorphism of blood protein and enzyme was investigated,and genetic co-adaptability among structural genes was studied in three goat populations(147 goats) including Chaidamu goat(CS), Chaidamu Cashmere goat(CRS) and Liaoning Cashmere goat(LRS) in Qinghai Province, China. The results were showed that the genetic disequilibrium of 10 locus combinations was found among 45 locus combinations in the three goat populations,and these genetic disequilibria were caused only by the difference of genetic co-adaptability among genes,because there didn't exist the linkage disequilibrium among non-allelic genes. The genetic disequilibrium including the difference of genetic co-adaptability between non-allelic genes was only found at Tf-P(A-3) locus combinations in LRS population,the other ones were all caused by the genetic disequilibrium at a single locus. The difference of genetic co-adaptability of LAP-EsD locus combinations could be messaged among different populations.