The abundance and distribution of cyanobacterial diazotrophs were quantified in two regions (Melanesian archipelago, MA and subtropical gyre, SG) of the Western Tropical South Pacific using nifH qPCR assays. UCYN-A1 and A2 host populations were quantified using 18S rRNA qPCR assays including one newly developed assay. All phylotypes were detected in the upper photic zone (0–50 m), with higher abundances in the MA region. Trichodesmium and UCYN-B dominated, composing 81–100 % of nifH copies detected. Het-1 was the next most abundant, and co-occurred with het-2 and het-3. The two UCYN-A lineages were least abundant (<1.0–1.5 % of total nifH copies) and poorly detected (> 47 %). Abundance of the UCYN-A hosts mirrored their respective symbionts; UCYN-A1 and A2 however were detected while their respective hosts were below detection, suggesting a lower partner fidelity or free-living life history. Pairwise comparisons of abundance and environmental parameters supported two groups: deep (45 m) comprised of UCYN-A and surface (0–15m) comprised of Trichodesmium, het-1 and het-2, while UCYN-B overlapped. Temperature, salinity, and PAR, were positively correlated with the latter abundances except UCYN-A. Similar results were identified in a meta-analysis of 11 external datasets. Combined, our results indicate that conditions favoring the UCYN-A symbiosis differ from those of diatom diazotroph associations and free-living diazotrophs.