Abstract The history of processing tomato industry in China is short and the major variety being used in production to date is still Riegel 87-5, a variety released in 1996. To investigate the genetic and fruit trait differences between Chinese elite lines/varieties and American varieties, 51 including 24 recently developed Chinese elite lines, four Chinese varieties, and 23 American varieties were subjected to genotypic analysis using 547 InDel markers. The range of Nei’s genetic distance was wider in Chinese elite lines (0.209–0.383) than in Chinese varieties (0.126–0.214) and American varieties (0.223–0.342). Cluster analysis indicated that the 51 varieties/lines could be classified into three groups without specific relationship between group and country. This was further supported by population structure analysis using the software STRUCTURE2.3.4. Fruit traits were collected from 51 tomato varieties/lines grown in 2013 and 2014. The average soluble solid content was lower, while the average fruit weight was larger, and the average color was relatively poorer in both Chinese elite lines and varieties than in the American varieties. However, some elite lines such as 9508-h and their progenies had relatively good fruit traits, and thus could be superior sources for processing tomato improvement. The experience of developing processing tomato industry in China could be of value to countries with similar situations.