Objective: To understand the pathogenic spectrum characteristics of enteroviruses of non-enterovirus (EV) 71 and non-coxsackievirus (CV) A16 associated with hand, foot and mouth disease (HFMD) in Xinjiang. Methods: Specimens were collected from HFMD patients infected with non-EV-A71 non-CV-A16 enterovirus from 2011 to 2016 in Xinjiang. The virion protein (VP)1 gene sequence was amplified by reverse transcription polymerase chain reaction (RT-PCR) and sequenced. Sequencing and genotyping were performed through erterovirus genotyping tool. Results: A total of 119 sequences were obtained, 15 human enterovirus serotypes were identified including CV-A6, CV-A10, CV-A4, CV-A8, CV-B1, CV-B3 (4 strains), CV-B4, CV-B5, ECHO30, ECHO12, ECHO14, CV-A9, CV-A24, PV1 and PV3. The composition ratio of CV-A6 among non-EV-A71 non-CV-A16 enterovirus in 2013, 2015 and 2016 was 87.9%, 79.5% and 88.3% respectively. Conclusions The pathogens causing HFMD in Xinjiang included more than 17 kinds of human enterovirus serotypes. Since 2013, CV-A6 has become the main pathogen of HFMD simultaneously or alternately with EV-A71 and CV-A16.