Significant advances have been made over the past decade on illustrating structural and functional features underneath the selective metal ion recognition by various proteins in nature. These efforts led to fruitful information regarding mechanisms that bacteria employed on the regulation, transportation, and utilization of main group and essential transition metal ions, and the detoxification of hazardous heavy metal ions. Here we summarize the recent advancement on the understanding of selective recognition of transition and heavy metal ions by metalloregulatory proteins. An emphasis is placed on demonstrating the molecular level mechanism of selective metal ion recognition in bacteria. Other types of metal sensory proteins will also be briefly reviewed.