Kreise and Gemeinden (or Ämter - sg.: Amt, which was the smallest sub-unit in Baden) developed independently from each other. Additionally, they developed in different ways depending on the state's constitution. For example, with the reforms during/after Napoleon's reign in central Europe, Prussia and Bavaria enacted laws to create and develop Gemeinden in their territory: In Bavaria, Gemeindeedikte WP, german were issued 1808 / 1818; in Prussia, the Städteordnung WP, german created a unified legal base for Gemeinden throughout the state.
The commune's most important peculiarity was their autonomy regarding certain tasks and competences that rest on a state in behalf of its citizens. In other words, the Gemeinde as organizational unit gave their citizens the means to regulate certain issues independently from the state's government, especially some fiscal matters. So, the primary "opposite" or counterpart of the Gemeinde wasn't the Kreis or Bezirk, but the state. Belonging to a certain Kreis was primarily an administrative issue without grave political consequences. The main issue was the relationship of the Gemeinden regarding the state, the distribution of power and political authority and amount of fiscal autonomy between state and Gemeinde. In modern times, distribution of competences between Gemeinden and upper-level bodies like Kreise or Bezirke is a matter of dispute quite often (esp. since those questions affect the economic autonomy of the Gemeinde), but i doubt whether this was true already during the 19th century.
The Kreise were partly established in the same time (e.g. in Baden), partly later, e.g. in Prussia beginning in 1880, in Bavaria as Bezirke (later, Bavaria divided the Bezirke into Kreise). WP Commons has a nice map illustrating the situation of the Reich in the year 1900. German Wikipedia has a complete list of the Kreise that were established in the different states of the German Reich.
So: yes, Gemeinden already existed in the German Reich, but not necessarily as a part of Kreise. Since Kreise served as a means to "encapsulate" multiple smaller units, i wouldn't expect to find a Kreis encompassing only one Gemeinde. Instead, even nowadays, there's the concept of kreisfreie / kreisunmittelbare Stadt (literally "circle-independent city") - that's a city that doesn't belong to a Kreis, but fulfils the tasks of a Kreis itself.