How are you importing Atomikos in your project? Using the starter:

<dependency>
  <groupId>com.atomikos</groupId>
  <artifactId>transactions-spring-boot3-starter</artifactId>
  <version>6.0.0</version>
</dependency>

I notice that transaction-jdbc, transaction-jms and transaction-jta are automatically imported with jakarta as classifier, thus having transaction-jdbc-6.0.0-jakarta.jar and so on in classpath.

Looking in the repo directory (https://repo1.maven.org/maven2/com/atomikos/transactions-jta/6.0.0/) in fact there are two different jars.

Check if you are importing the "no-jakarta" modules, and in this case try to use the starter, or specify the classifier in pom.xml, like this:

<dependency>
  <groupId>com.atomikos</groupId>
  <artifactId>transactions-jta</artifactId>
  <version>6.0.0</version>
  <classifier>jakarta</classifier>
</dependency>