On my local KinD cluster, I deployed:

• Prometheus using kube-prometheus-stack, everything with default values.
• Thanos using Bitnami’s chart, and the following values file:

query:
  enabled: true
  logLevel: debug
  dnsDiscovery:
    enabled: false
  stores:
    - thanos-ruler.prometheus.svc.cluster.local:10901
  resources:
    limits:
      cpu: 100m
      memory: 256Mi
    requests:
      cpu: 50m
      memory: 128Mi

ruler:
  enabled: true
  logLevel: debug
  clusterName: local-ruler
  alertmanagers:
    - http://prometheus-kube-prometheus-alertmanager.prometheus.svc.cluster.local:9093
  config: |-
    groups:
      - name: example
        rules:
          - alert: HighCPUUsage
            expr: 100 - (avg by(instance) (rate(node_cpu_seconds_total{mode="idle"}[2m])) * 100) > 80
            for: 5m
            labels:
              severity: warning
            annotations:
              summary: High CPU usage detected
  resources:
    limits:
      cpu: 100m
      memory: 256Mi
    requests:
      cpu: 50m
      memory: 128Mi

metrics:
  enabled: true
  serviceMonitor:
    enabled: true
  prometheusRule:
    enabled: false

objstoreConfig: |-
  type: FILESYSTEM
  config:
    directory: /tmp/thanos/object-storage

When I port-forward svc/thanos-query-frontend and check “Rules”, I only see the static HighCPUUsage rule I deployed along with the Thanos Ruler.
However, I also applied a another rule:

apiVersion: monitoring.coreos.com/v1
kind: PrometheusRule
metadata:
  name: test-rule
  namespace: prometheus
  labels:
    release: prometheus
spec:
  groups:
  - name: test.rules
    rules:
    - alert: Suka
      expr: vector(1) == 1
      for: 5s
      labels:
        severity: warning
      annotations:
        summary: "This is a test alert"
        description: "This is a test alert"

I’d expect to see this rule under Thanos as well, but I only see it in the Prometheus instance. I’m not sure what I’m misunderstanding with my setup.