A system and computer-implemented method are provided for host level detection of malicious Domain Name System (DNS) activities in a network environment having multiple end-hosts. The system includes a set of DNS resolver agents configured to (i) gather DNS activities from each of the multiple end-hosts by recording DNS queries and DNS responses corresponding to the DNS queries, and (ii) associate the DNS activities with Program Identifiers (PIDs) that identify programs that issued the DNS queries. The system further includes a backend server configured to detect one or more of the malicious DNS activities based on the gathered DNS activities and the PIDs.