Recent studies have shown that there are geographic variation of alpha-neurotoxins in Naja kaouthia, but the cause is not clear yet. In this work, venoms were collected from adult Naja atra in Zhejiang Province and Naja kaouthia in Yunnan Province, well identified by morphological characters and cytochrome b gene analysis in summer season to avoid age and seasonal variation in the venom composition. Then alpha-neurotoxins were purified and cloned from these two kinds of snakes. Three alpha-neurotoxins from Naja kaouthia (Yunnan) and two from Naja atra (Zhejiang) were identified. Together with previously reported alpha-neurotoxins in Naja kaouthia (Thailand) and Naja atra (Taiwan Province), it was found that the alpha-neurotoxins of Naja kaouthia in Yunnan Province were similar to those of Naja atra in Zhejiang and Taiwan Provinces, but different from those of Naja kaouthia in Thailand. This result can hardly be explained by population phylogeny or geographic distance. It might be due to the different climate, habitat and prey in Thailand in comparison with those in Yunnan, Zhejiang and Taiwan Provinces.