It becomes plainer in the context of the whole passage. I think it's clear that he's talking about the 'minor=sad, major=happy' thing. Interesting that he also considers diatonic notes 'masculine and virile', chromatics as 'effeminate and languishing'.
I'm not sure we have enough extant material to judge whether Morley's language was normal for the time. But I remember being taught about 'masculine' and 'feminine' phrase endings. Have they now been replaced by something more politically correct?
"It now followeth to show you how to dispose your music according to the nature of the words which you are therein to express, as whatsoever matter it be which you have in hand such a kind of music must you frame to it. You must therefore, if you have a grave matter, apply a grave kind of music to it, if a merry subject you must make your music also merry, for it will be a great absurdity to use a sad harmony to a merry matter or a merry harmony to a sad, lamentable, or tragical ditty [i.e., text].
You must then when you would express any word signifying hardness, cruelty, bitterness, and other such like make the harmony like unto it, that is somewhat harsh and hard, but yet so that it offendeth not. Likewise when any of your words shall express complaint, dolour, repentance, sighs, tears and such like let your harmony be sad and doleful. .So that if you would have your music signify hardness, cruelty, or other such affects you must cause the parts proceed in their motions without the half step, that is, you must cause them proceed by whole steps, sharp thirds, sharp sixths, and such like; you may also use cadences bound with dissonances which, being in long notes, will exasperate the harmony. Rut when you would express a lamentable passion then must you use motions proceeding by half steps, flat thirds, and flat sixths, which of their nature are sweet, specially being taken in the true tune with discretion and judgment.
But those chords so taken as I have said before are not the sole and only cause of expressing those passions, but also the motions which the parts make in singing do greatly help; which motions are either natural or accidental. The natural motions are those which are naturally made betwixt the notes of the scale without the mixture of any accidental sign or chord, be it either flat or sharp, and these motions be more masculine, causing in the song more virility than those accidental chords which are marked with the sharp and the flat, which be indeed accidental and make the song, as it were, more effeminate and languishing than the other motions which make the song rude and sounding. So that those natural motions may serve to express those effects of cruelty, tyranny, bitterness, and such others, and those accidental motions may fitly express the passions of grief, weeping, sighs, sorrows, sobs, and such like."