<p>While inbreeding is known to affect individual fitness and thus population extinction risk, studies often under-represent non-model species of conservation concern and rarely examine the conditionality of inbreeding depression. Here, using genomic markers (SNPs), we determined inbreeding depression in a threatened bird, the aquatic warbler <i>Acrocephalus paludicola</i> – a habitat specialist with depleted genetic diversity that went through a steep recent decline. We also explored whether the magnitude of inbreeding depression depends on phenotypic (tarsus and wing length) and environmental (timing of breeding and brood size) factors. In adult males, the relationship between genomic inbreeding and breeding success depended on tarsus length, a proxy for body size, being strongly negative in small-tarsus males. We also detected a weak interaction effect between genomic inbreeding and wing length on male survival, with short-winged males being negatively affected by inbreeding. By contrast, models that did not include these interactions provided little evidence for inbreeding effects on male fitness, and estimates of inbreeding load were highly uncertain for both survival and breeding success. In adult females, we found little support for associations between genomic inbreeding and clutch size, hatching success, nestling survival, or fledged brood size, and no evidence that these relationships were conditional on the phenotypic and environmental variables examined. Accordingly, estimates of inbreeding load in females were close to zero. We conclude that inbreeding depression on fitness components is phenotype-dependent, being stronger in small-bodied males, and that considering interactions with phenotypic variables enables more accurate estimation of inbreeding depression.</p>