When deploying Trojan-based VPN/proxy solutions, DNS resolution problems are among the most common and often the most subtle issues administrators and developers encounter. Resolving DNS issues in a Trojan setup requires understanding how DNS requests traverse the host stack, the VPN/proxy client, and the network, as well as how the system resolver and DNS caching services behave. This article provides practical troubleshooting steps, quick fixes, and best practices tailored for site operators, enterprise administrators, and developers who rely on Trojan deployments.

Why DNS Issues Happen with Trojan

Trojan is a TLS-based proxy designed to look like HTTPS traffic. When used as a system-wide proxy or VPN (via tools like trojan-go, GUI clients, or system-level redirection), DNS can break for several reasons:

  • Local system resolvers continue to use the ISP DNS and leak requests.
  • DNS queries are sent over UDP and bypass the TCP/TLS tunnel that Trojan uses, causing blocked or inconsistent resolution.
  • Split-tunneling or firewall rules route only TCP traffic through the proxy, leaving DNS over UDP unsent.
  • Misconfigured DNS forwarders (dnsmasq, systemd-resolved) interact poorly with the proxy’s expectations.
  • DNS caching and negative caching present stale entries or cache poisoning symptoms.

Rapid Diagnostic Checklist

Before changing configurations, gather diagnostic facts. The following checks will quickly reveal the scope of the problem.

  • Resolve with dig/nslookup/getent: Run dig +short @8.8.8.8 example.com and dig +short example.com to compare direct upstream resolution vs system resolver.
  • Check /etc/resolv.conf: Verify the configured nameserver entries and whether they point to a local resolver like 127.0.0.53 (systemd-resolved) or an external IP.
  • Test TCP vs UDP DNS: Use dig +tcp example.com to see if TCP-based DNS works while UDP fails.
  • Check for DNS leaks: Use online leak tests or packet captures to see if DNS requests go to the ISP when they should go through the proxy.
  • Check Trojan logs: Enable verbose debug in trojan/trojan-go; look for TLS handshake errors or connection resets related to DNS upstream IPs.
  • Packet capture: Use tcpdump -i any port 53 or Wireshark to trace DNS packets and determine routing and protocol (UDP/TCP/DoT/DoH).

Quick Fixes: Fast Remedies That Often Work

If you need immediate remediation for an operational environment, try these targeted fixes in order. They are safe to apply with minimal disruption.

1. Force DNS via the Tunnel (Use TCP/DoT/DoH)

Since Trojan proxies TCP/TLS traffic, forcing DNS over TCP, DoT (DNS over TLS), or DoH (HTTPS) ensures queries traverse the tunnel. Quick options:

  • Configure your local resolver to use a DoT upstream (e.g., 1.1.1.1:853) or DoH endpoint (Cloudflare, Google).
  • Use a DNS client that supports DoH, such as cloudflared or dnscrypt-proxy, and bind it to localhost. Point system resolv.conf to that local instance.

2. Redirect UDP DNS to TCP via iptables

On Linux, you can redirect UDP DNS to TCP to force resolver clients to use TCP, which parents through the proxy more reliably:

  • Example iptables rule: iptables -t nat -A OUTPUT -p udp --dport 53 -j REDIRECT --to-ports 5353 with a local DNS proxy listening on 5353 that performs TCP/DoT upstreams.
  • Use nftables equivalent when nft is your primary framework.

3. Disable systemd-resolved or Replace with dnsmasq

systemd-resolved can complicate DNS flow (split DNS, Link-specific). If Trojan clients misbehave with it active, switch to dnsmasq or a dedicated DoH/DoT client:

  • Stop systemd-resolved: systemctl disable --now systemd-resolved (careful on systems that rely on it).
  • Install dnsmasq and bind to 127.0.0.1; update /etc/resolv.conf to nameserver 127.0.0.1.

4. Add Static Host Entries for Critical Services

If certain domains fail to resolve during troubleshooting and you need a stopgap, add /etc/hosts entries for critical endpoints. This is temporary and not a long-term solution, but it helps restore essential connectivity.

Deep Troubleshooting: Root Cause Analysis

When quick fixes don’t suffice, follow a structured approach to uncover systemic causes. This section outlines deeper checks and configuration adjustments.

Inspect Client and Server Logs

Enable debug logs on both the Trojan client and the server-side. Look specifically for:

  • Connection resets when the client attempts to reach upstream DNS servers.
  • TLS handshake failures that could be mistaken for DNS errors.
  • Frequent reconnections that signal packet loss or MTU issues affecting DNS over UDP/TCP.

Validate Firewall and NAT Rules

Many DNS problems are caused by firewall rules that inadvertently block outbound traffic to public DNS servers or prevent UDP replies. Verify:

  • Outbound policies allow UDP/53 and TCP/53 to chosen upstreams if needed.
  • SNAT/MASQUERADE rules do not alter source IPs in a way that breaks DNS server expectations.
  • Packet fragmentation and MTU settings are consistent, particularly when DNS responses are larger (e.g., DNSSEC).

Check DNS Caching and Negative Cache

DNS caches (both local and remote) can serve stale or negative results. Flush caches where possible:

  • systemd-resolve --flush-caches for systemd-resolved.
  • Restart dnsmasq: systemctl restart dnsmasq.
  • Ensure caching software obeys TTLs and respects DNSSEC validation if enabled.

Use Network-Level Traces

Packet capture is essential to see what actually leaves the host. Check for:

  • DNS queries leaving on the wrong interface (e.g., the LAN instead of the VPN tunnel).
  • DNS replies being dropped by an intermediate firewall.
  • Unexpected responses or NXDOMAIN from local resolvers indicating misconfiguration.

Configuration Patterns and Best Practices

After fixing immediate issues, adopt these best practices to minimize future DNS problems in Trojan environments.

Prefer Encrypted DNS Aligned with Trojan’s Transport

Always prefer DNS over an encrypted transport that matches the proxy tunnel characteristics—DoT or DoH. This prevents DNS leakage and ensures the resolver traffic follows the same path as other proxied TCP/TLS traffic.

Run a Local Resolver/Forwarder

Deploy a local resolver such as dnsmasq, Unbound, or a DoH/DoT client bound to localhost. Benefits:

  • Centralized control of upstreams and caching.
  • Ability to force TCP/DoT/DoH and to filter or block undesired domains before they leave the host.
  • Seamless integration with iptables redirection if necessary.

Harden Resolver Settings

Configure your resolver with the following considerations:

  • Enable DNSSEC validation where possible to avoid spoofing.
  • Limit concurrency and rate limits to protect upstreams and avoid transient failure amplifications.
  • Set sane cache TTLs to balance freshness and query load.

Integrate DNS into Proxy/BYPASS Rules

If you use domain-based routing or bypass lists, ensure DNS resolution logic aligns with the routing rules. For example, if a domain is meant to bypass the proxy, local resolution should be forced rather than routed over Trojan. Conversely, sensitive domains should always resolve via encrypted channels.

Tools and Commands You Should Have in Your Kit

  • dig/nslookup — compare different upstreams and protocols.
  • tcpdump/tshark — capture DNS traffic and verify routing.
  • systemd-resolve — inspect systemd-resolved status and caches.
  • iptables/nft — inspect and control DNS redirection rules.
  • trojan/trojan-go logs — verbose logs for TLS/proxy diagnostics.
  • Wireshark — visual analysis for complex packet-level issues.

Common Pitfalls and How to Avoid Them

Some recurrent mistakes produce intermittent DNS failures:

  • Relying on UDP-only DNS in environments where UDP is blocked or selectively dropped. Avoid by enabling TCP/DoT/DoH.
  • Assuming /etc/resolv.conf semantics are static. On modern Linux systems, network managers and systemd-resolved may overwrite it.
  • Forgetting split-DNS for internal corporate zones, leading to leakage or failed resolution when tunneled to public resolvers.

Conclusion

Troubleshooting DNS with Trojan requires a methodical approach: verify where queries are sent, ensure DNS uses transports that match the proxy’s capabilities (TCP/DoT/DoH), and consolidate resolution through a local resolver or forwarder when possible. Use packet captures and logs to confirm behavior and adopt best practices—encrypted DNS, local caching, and careful firewall rules—to avoid recurring issues.

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