The World Health Organization (WHO) declared the COVID-19 outbreak a “Public Health Emergency of International Concern” on 30 January 2020, after rapid spread from a few initial cases to thousands of cases across China and introductions into several other countries. On 11 March 2020, the WHO classified the outbreak as a pandemic. The first cases in Switzerland, Basel-Stadt, and Basel-Landschaft were confirmed on 25 February, 27 February and 28 February 2020. As of 22 April 2020, there are 28,154 confirmed cases in Switzerland, including 933 and 811 in the Cantons of Basel-Stadt and Basel-Landschaft, respectively. The rapid increase of confirmed cases in March suggests considerable community transmission. We estimated the reproductive number through time for the whole of Switzerland and its cantons for which sufficient data are available. For this estimation, we used publicly available data on the number of confirmed cases and COVID-related deaths through time, as well as additional data directly obtained from the University Hospital of Basel and the Cantonal Office of Public Health, Economics and Health Directorate of Basel-Landschaft. If the reproductive number is below 1, the epidemic is overall under control for that specific location, with the number of new infections per day decreasing through time. If this number is above 1, the epidemic is exponentially increasing in size. We found that the reproductive number in Switzerland was between 1.5 and 2 during the first third of March, and has consistently decreased to around 1. After the announcement of the latest strict measure on 20 March 2020, namely that gatherings of more than five people in public spaces are prohibited, the reproductive number dropped significantly below 1, we estimated the reproductive number to be between 0.6 and 0.8 in the first third of April. Our sensitivity analyses addressed the concern of a decreasing reproductive number being merely an artifact of less intense testing through time. In summary, our results suggest that from the last week of March onwards, the reproductive number was significantly below 1 in Switzerland and thus the epidemic was declining. However, our analyses do not allow us to identify a cause for this decline. From now on, we will provide daily estimates for the reproductive number on our webpage. Important to note in this respect is that estimates of the reproductive number lag about 10 days behind the last date of data collection since confirmation of the diagnosis occurs around 10 days after infection.