Although there have been described alterations of circadian rhythmicity both in patients with substance use disorder (SUD) and patients with major depressive disorder (MDD), the circadian characteristics of SUD patients with comorbid MDD (SUD-MDD) are unknown. Likewise, the possible influence of the different modalities of treatments (ambulatory or therapeutic community) upon the circadian rhythmicity of SUD patients has not been characterized. Therefore, this study analyzes the circadian rhythmic profiles of SUD and SUD-MDD patients under ambulatory and therapeutic community treatment. The sample was composed of 40 SUD and 40 SUD-MDD men, aged 22-55 yrs, under treatment and with abstinence for at least three months (including each group 20 ambulatory and 20 from therapeutic community). Patients completed a sociodemographic, clinical and sleep-wake schedules interview, the Composite Scale of Morningness, and wore on the wrist an ambulatory device known as iButton® Thermochron DS1921H, which registered their distal skin temperature every two minutes for 48 hours. All the groups showed a tendency to morningness without differences among them in concordance with their sleep-wake schedules. With regard to distal skin temperature circadian rhythm, SUD patients showed higher values than SUD-MDD in amplitude, relative amplitude, percentage rhythm, and first harmonic power, and lower minimum temperature in 10 consecutive hours (p < .043, in all cases). Therapeutic community group values were lower in minimum temperature and higher in amplitude, relative amplitude, and 12 harmonic accumulated power (p < .028, in all cases) as compared to ambulatory ones. Moreover, all groups showed higher Rayleigh vector and rhythm stability as compared to normative population (p < .043, in both cases). The circadian rhythmic differences observed for diagnosis and type of treatment are indicative of a higher circadian rhythmicity robustness in SUD and therapeutic community patients as compared to SUD-MDD and ambulatory ones, respectively. Although drug consumption exerts a negative effect on the circadian rhythmicity, our results (high amplitude and rhythm stability) are indicative of an adequate circadian functioning as well as of an adjustment to the light-dark cycle in both diagnosis and type of treatment which may constitute a marker of the adherence to treatment and recovery status.