Using data from 27 seismograph stations for the period 1990-2001, we have relocated 106 hypocenters of earthquakes with magnitudes from 0.9 to 5.4 in the region of the southern Great Lakes. Two complementary methods were used for relocation: a conventional least-squares approach (Lienert and Havskov, 1995) and joint hypocentral determination (Pujol, 2000). These two methods yielded mutually consistent spatial patterns of seismicity with an average difference of 3.7 km in epicentral locations and 1.1 km in focal depths. We show that the hypocenter locations are not very sensitive to realistic uncertainties in 1D crustal velocity. Our sharpened definition of zones of seismicity delineates several clusters beneath Lake Ontario, around Niagara Falls, and near the south shore of Lake Erie. These seismicity zones appear to correlate with areas where the regional magnetic data exhibit prominent short-wavelength (<5 km) linear anomalies. The magnetic anomalies are associated with basement structures that formed during the Precambrian (Mesoproterozoic) Grenville orogen. Both the seismicity and magnetic anomalies exhibit statistically significant preferred orientations at N40°E-N45°E, but the correlation of the earthquake clusters with specific aeromagnetic lineaments remains uncertain. Three preliminary focal mechanisms of earthquakes with magnitudes mN 3.1 to 3.8 show unusual normal faulting, with nodal planes in almost the same direction as the magnetic trends, N42°E-N52°E. Proximity of the earthquake clusters to large bodies of water, coupled with colinearity with magnetic anomaly trends, suggests that both surface water and pre-existing basement structures may play significant roles in controlling intraplate seismicity in the southern Great Lakes region.