Intestine contains the body's second largest genetic information, so a relatively stable microbiota ecosystems and interactions between intestinal micro-organisms play a pivotal role in the normal growth and development in animals. The establishment of intestinal microflora is affected by a variety of factors such as species, environmental factors, developmental stage, organizational structure and physiological characteristics of various parts of the digestive tract. Gene editing technology such as ZFN has recently been used as a new approach to replace the traditional transgenic technology and to make genetic modifications in animals. However, it is not known if genetic modification by gene editing technology will have any impact on gut microbiota. In this study, by sequencing 16S rRNA collected from rectum, we investigated the effects of ZFN-mediated myostatin (MSTN) loss-of-function mutation (MSTN-/-) on gut microbiota in Meishan pigs. Our results showed that the fecal microbial composition is very similar between MSTN-/- Meishan pigs and wild type Meishan pigs. Although significant differences in certain individual strains were observed, all the dominant microorganism species are basically the same between MSTN-/- and wild type pigs. However, these differences do not adversely affect MSTN-/- Meishan pigs. Thus, it is concluded that ZFN-mediated MSTN loss-of-function mutation did not have any adverse effect on the gut microbiota in Meishan pigs.