Summary Anaerobic ammonium oxidizers contribute to the removal of fixed nitrogen in oxygen‐deficient marine ecosystems such as oxygen minimum zones ( OMZ ). Here we surveyed for the first time the occurrence and diversity of anammox bacteria in the C olombian P acific, a transition area between the prominent S outh and N orth P acific OMZs . Anammox bacteria were detected in the coastal and oceanic areas of the C olombian P acific in low oxygen (< 22 μM), high nitrate (25–35 μM) and low nitrite (< 0.07 μM), and ammonium (< 1 μM) waters. In these waters, anammox bacteria were rich [∼ 7 operational taxonomic units ( OTUs ), 98% cut‐off) and microdiverse ( S hannon index H ′ < 1.24), in comparison with the observed at the prominent OMZ of the E astern T ropical S outh P acific, A rabian S ea and B lack S ea. Anammox bacteria‐like sequences from the C olombian P acific were grouped together with sequences retrieved from the distinct OMZ 's marine subclusters ( P eru, N orthern C hile and A rabian S ea) within C andidatus ‘ S calindua spp’. Moreover, some anammox bacteria OTUs shared a low similarity with environmental phylotypes (86–94%). Our results indicated that a microdiverse anammox community inhabits the C olombian P acific, generating new questions about the ecological and biogeochemical differences influencing its community structure.