Multiple testing of unbalanced data by R
It sounds like you are using Welch's t-test to compare groups of different sizes. That should work in your situation. It's more reliable that the standard Student's t-test when you have unequal variances and unequal sample sizes.

Note that sample sizes do not have to be identical for a Student's t-test. The important thing is that the variances are the same. If the variances are not equal, this is where the extra robustness of Welch's becomes helpful.

Whether or not you can conclude significance depends on what P-value you are you are looking for. It sounds like you are targeting p&lt;.01, so if your result is less than .01, you can report that you found a significant difference.