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Ex situ conservation breeding for species recovery often must address small founder number. Here we investigated the long‐term effects of small founder size in the endangered black‐footed ferret Mustela nigripes using 20 years of reproductive data. Specifically, we studied seminal traits, pregnancy success and litter size in the context of the population's low genetic diversity. Detailed evaluation of 539 electroejaculates from 262 pedigreed donors with varied inbreeding coefficients (F = 0.000–0.250) revealed a wide range in sperm motility (0.0–100.0%), forward progression (type of forward movement on a scale 0–5; 5 = best; 0.0–4.5), cell concentration (7.2–6348.0 × 106 mL−1 of ejaculate), structural normality (0.0–89.0%) and normal apical ridges (critical for fertilization; 4.8–100.0%). Over this two decade interval, there was an increase (P < 0.05) in F and a decrease (P < 0.05) in sperm forward progression and structurally normal cell morphology. From analysis of artificial insemination (AI) data, higher values for sperm motility, forward progression and structural normality or spermatozoa that retained a normal apical ridge had a positive influence (P < 0.05) on litter size. Males producing higher values for these four traits also sired more kits. Results demonstrate that sperm motility and morphology are decreasing in black‐footed ferrets managed intensively ex situ. These two metrics appear associated with an increasing F and likely are at least partially responsible for lowered reproductive success in this closed, endangered population. These results illustrate the potential physiological and offspring production impact of having few founders available in an ex situ conservation breeding program. [ABSTRACT FROM AUTHOR]