Start at Plateia Venizelou, the large clearing at the far curve of the old harbor -- now distinguished by its marble fountain. Head along the east side to see the prominent domed Mosque of Djamissis (or of Hassan Pasha), erected soon after the Turks conquered Chania in 1645. Proceeding around the waterfront toward the new harbor, you'll come to what remains of the great arsenali, where the Venetians made and repaired ships; exhibitions are sometimes held inside. Go to the far end of this inner harbor and if you are lucky (due to unpredictable hours) you can enter the old arsenal and see the massive replica of a Minoan ship that was made to participate in the Athens Olympics of 2004; they actually got a crew of about 24 to row it (stage by stage) to Piraeus but the authorities deemed it not authentic and it never got much recognition. In any case, you can walk out along the breakwater to the 19th-century lighthouse (thoroughly restored in 2006). Go back to the far corner of the long set of arsenali and Arnoleon, where you turn inland and then proceed up Daskaloyiannis; on the left you'll come to Plateia 1821 and the Orthodox Church of St. Nicholas. Begun as a Venetian Catholic monastery, it was converted by the Turks into a mosque -- thus its campanile and minaret! (It has also been undergoing a major restoration which should be finished by 2008.) The square is a pleasant place to sit and have a cool drink. Go next to Tsouderon, where you turn right and (passing another minaret) arrive at the back steps of the great municipal market (ca. 1911) -- worth wandering through, although, and alas, it too is being taken over by touristic shops.
If you exit at the opposite end of your entrance, you'll emerge at the edge of the new town. Go right along Hadzimikhali Giannari until you come to the top of Halidon, the main tourist-shopping street. The stylish Municipal Art Gallery, at no. 98, sits at the top right side (hours posted). As you continue to make your way, you'll pass on the right the famous Skridlof, with its leather workers; the Orthodox Cathedral or the Church of the Three Martyrs, from the 1860s; and on the left the Archaeological Museum.
As you come back to the edge of Plateia Venizelou, turn left one street before the harbor onto Zambeliou. Proceed along this street; you can then turn left onto any of the side streets and explore the old quarter (now, alas, overwhelmed by modern tourist enterprises). If you turn up at Kondilaki, follow the signs at the right alley for the synagogue; built in the 17th century and destroyed in World War II, it has now been beautifully restored and is well worth a visit. (Check www.etz-hayyim-hania.org to learn about the history and activities of the synagogue.) Continue along Zambeliou, but take a slight detour to Moskhou to view Renieri Gate from 1608. On Zambeliou again, you'll ascend a bit until you come to Theotokopouli; turn right here to enjoy the architecture and shops of this Venetian-style street as you make your way down to the sea.
At the end of the street, on the right, the recently restored Church of San Salvatore was converted into a fine little museum of Byzantine and post-Byzantine art (irregular hours; admission 2€/$2.60 (www.culture.gr). After the museum, you'll be just outside the harbor; turn right and pass below the walls of the Firkas, the name given to the fort that was a focal point in Crete's struggle for independence at the turn of the 20th century. If you're into naval history, the Naval Museum (tel. 28210/26-437) here has some interesting displays and artifacts (daily 10am-4pm; admission 5€/$6.50); or you can take a seat for welcome refreshment at one of the cafes on the slope before the museum entrance.