When the east and west German rail companies, Deutsche Reichsbahn and Deutsche Bundesbahn, merged on 1 April 1993, their ferried services were also amalgamated and Deutsche Fährgesellschaft Ostsee mbH (DFO) founded as a private company. The new shipping line continued to expand its existing route network and intensified cooperation with its long-term Danish and Swedish shipping line partners, Scandlines A/S and Scandlines A/B respectively.
The fleet was extensively modernised, with the commissioning of new, modern ferries setting standards in the market. For example, the "Mecklenburg – Vorpommern”, which went into operation in December 1996, is still one of the largest combined passenger/trailer/rail ferries in the world, while the double-ended ferries, the "Deutschland" and "Schleswig-Holstein", commissioned in 1997, have reduced the crossing time on the popular “Vogelfluglinie” between Puttgarden and Rødby by 25% to just 45 minutes.
This merger of the former shipping line partners, DFO and Scandlines A/S, resulting in the founding of Scandlines AG on 21 July 1998 conferred a new quality on the almost century-long cooperation between the Danish and German rail services and their successor companies. Two partners who have always worked together - despite two world wars and 40 years of a divided Germany - were now united in a single joint enterprise.
Brief outline of further developments at Scandlines AG:
- November 1998 - Deutsche Fährgesellschaft Ostsee mbH (DFO) renamed Scandlines Deutschland GmbH
- 1 January 1999 - Acquisition of 40% of the shares of the company Mols - Linien A/S
- 1 May 1999 – Acquisition of the Ro-Ro liner service “Balticum Seaways”
- 17 June 1999 – Opening of the first Border Shop in Puttgarden
- 10 August 1999 – Acquisition of the shipping line Euroseabridge GmbH – Ferry Services (renamed Scandlines Euroseabridge GmbH on 1 January 2000)1 January 2000)
- 1 November 1999 – Cooperation agreement between Euroseabridge and LISCO with a joint service departing from Kiel under the name “Kiel - Klaipeda Express”
- 31 November 1999 – Acquisition of MSC Mitropa Schiffs Catering GmbH, renamed Scandlines Catering GmbH
- 1 December 2000 – Opening of an office in Holland for cargo customers from the Benelux region
- 1 February 2000 – Reorganisation of the Rostock – Liepaja link into a cargo/passenger line
- 14 August 2000 – Opening of Scandlines agency in Berlin
- 11 December 2000 – Acquisition of the Rostock Port Center
- 1 Mai 2001 – Introduction of 3rd
vessel on the Rostock – Gedser line
- 19 May 2001 – Opening of the new Border Shop in Puttgarden
- May 2001 - Refitting of the FS “Ask” – expansion of passenger and cargo capacities on the Rostock - Liepaja line
- September 2001 – Refitting of the FS “Urd”
- 4 December 2001 – Opening of the Ship Simulation Centre in Puttgarden
- 14 May 2003 - the Puttgarden-Rødby VogelflugLine celebrates its 40th anniversary
- 26 June 2003 - Scandlines takes over the operations of T&E ESCO RORO Line AS (renamed Scandlines Estonia AB) / expansion of the Scandlines route network to include the Rostock-Helsinki and Helsinki-Muuga cargo links
- 24 July 2003 - Scandlines opens the Nynäshamn (Sweden) - Ventspils (Latvia) ferry service
- 30 September 2003 - Scandlines celebrates the 10th anniversary of the launch of the Rostock-Gedser line
- 5 December 2003 – Opening of the 2nd Border Shop in Germany at the Sassnitz Ferry Terminal
- 1 January 2004 – Merger of Scandlines Euroseabridge GmbH with Scandlines Deutschland GmbH
- 4 February 2004 – 10th anniversary of the Rostock – Liepaja service
- 27 June 2004 - 10th anniversary of the Rostock – Trelleborg service
- 6 July 2004 – 95th anniversary of the launch of the Sassnitz – Trelleborg rail ferry crossing
- 31 October 2004 – Last voyage of the FS "Rügen" / closure of the Sassnitz-Rønne (Island of Bornholm) ferry link
- 31 December 2004 – Discontinuation of the Rostock – Helsinki ferry service
Passenger 
