Studies on the reproductive endocrinology of koalas have been performed mainly by using blood samples; however, in practice it is difficult to collect blood periodically because koalas are easily stressed. The purposes of the present study were to establish a noninvasive endocrine monitoring technique and to investigate the reproductive physiology of female koalas. Feces were collected from female northern and southern koalas, and progestagen was extracted from lyophilized fecal samples and determined by enzyme immunoassay. In nonpregnant northern and southern koalas, fecal progestagen markedly increased after copulation and remained high for 36.3 ± 2.5 days and 38.9 ± 1.4 days (luteal phase, mean ± SEM), respectively. Mean (±SEM) progestagen levels (6.34 ± 0.49 μg/g) during the luteal phase in northern koalas were significantly higher than in southern koalas (4.19 ± 0.24 μg/g). Fecal progestagen in parturient northern koalas remained high for 36.2 ± 1.9 days (gestation period, 34.1 ± 0.3 days). In northern koalas, the mean levels and profiles of progestagen during pregnancy (6.44 ± 0.37 μg/g) were consistent with those during nonpregnancy after copulation (6.34 ± 0.49 μg/g). The duration of behavioral estrus in northern koalas was 13.5 ± 0.9 days without copulation. In contrast, when estrous females mated, the estrous sign disappeared just after copulation. The mean (±SEM) length of the estrous cycle in northern koalas, as determined by behavioral estrus intervals, was 33.5 ± 2.2 days without the luteal phase and 69.2 ± 7.6 days with the luteal phase. Fecal progestagen analysis is a helpful and noninvasive tool to monitor ovulatory activity in northern and southern koalas and could help us to understand the reproductive activity of koalas by the combination approach with behavioral estrus.